Genetic markers for predicting responsiveness to therapy with hdl-raising or hdl mimicking agent

ABSTRACT

Genotyping methods and compositions for selecting patients with cardiovascular disease who will benefit from treatment with HDL-raising or HDL mimicking agent, in particular with a CETP inhibitor/modulator

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a Continuation of U.S. application Ser. No.15/415,112, filed Jan. 25, 2017, now U.S. Pat. No. 10,584,385, which isa Continuation of International Application No. PCT/EP2015/067098 filedon Jul. 27, 2015, which is entitled to the priority of EP ApplicationNo. 14179048.5 filed on Jul. 30, 2014, the disclosures of which areincorporated herein by reference.

FIELD OF THE INVENTION

The field of the invention relates to the treatment or prophylaxis ofsubject with cardiovascular disorder.

BACKGROUND OF THE INVENTION

Although 20 years ago, one treatment fits all was the approach takenwhich led to formidable “blockbuster” drugs. Today with the sequencingof the human genome and advances in molecular profiling technologies,approaches to drug development are taking a more stratified orpersonalized approach. These advances increasingly allow forclassification of individuals into subpopulations that are at risk of aspecific disease, respond to a specific treatment, don't respond to aspecific treatment or are at high risk of an adverse event when treated.As such genetic tests can be used to inform diagnosis, prognosis andtreatment selection. Numerous studies have shown a relationship betweengenotype and response to pharmaceutical therapies. This approach hasbeen widely embraced over the past years, particularly in oncology wherenumerous personalized medicine approaches have been successfullydeveloped and have provided major improvement in clinical outcomes.

In cardiovascular disorders the stratification of the population bygenotype for a specific therapeutic intervention has been limited. Oneof the objectives of the present invention is to demonstrate that thepopulation suffering from cardiovascular disorders might behavedifferently and consequently may respond differently to a specifictreatment. Lowing LDL is an important therapeutic strategy in themanagement of cardiovascular disease. Indeed statin drugs, which lowerLDL, such as Crestor, Lipitor, Pravachol, and Zocar are widely used andamong the most prescribed drugs. For some time it has also beengenerally accepted that increasing HDL could also be therapeutic incardiovascular disease. Several HDL-raising drugs have been developedincluding: niacin and CETP inhibitors such as torcetrapib, anacetrapib,evacetrapib and dalcetrapib.

Cholesterylester transfer protein (CETP) also called plasma lipidtransfer protein is a hydrophobic glycoprotein that is synthesized inseveral tissues but mainly in the liver. CETP promotes bidirectionaltransfer of cholesteryl esters and triglyceride between all plasmalipoprotein particles. The first evidence of the effect of CETP activityon plasma lipoproteins was provided by observations in people withgenetic deficiencies of CETP. The first CETP mutation was identified inJapan in 1989 as a cause of markedly elevated HDL-C. Ten mutationsassociated with CETP deficiency have since been identified in Asians andone in Caucasians. It was found in Japan that 57% of subjects withlevels of HDL-C>100 mg/dL have mutations of the CETP gene. In addition,37% of Japanese with levels HDL-C between 75-100 mg/dL have mutations ofthe CETP gene. Subsequently, studies of animals treated with ananti-CETP antibody showed that CETP inhibition resulted in a substantialincrease in the concentration of HDL-C. Consistent with theseobservations in CETP deficient patients and rabbits treated with ananti-CETP antibody, it has since been found that treatment of humanswith CETP inhibitor drugs increases the concentration of HDL cholesteroland apoA-I (the major apolipoprotein in HDLs). Numerous epidemiologicstudies have correlated the effects of variations in CETP activity withcoronary heart disease risk including studies of human mutations(Hirano, K. I. Yamishita, S. and Matsuzawa Y. (2000) Curr. Opin. Lipido.11(4), 389-396).

Atherosclerosis and its clinical consequences, including coronary heartdisease (CHD), stroke and peripheral vascular disease represents anenormous burden on health care systems internationally. Drugs thatinhibit CETP (CETP inhibitors) have been under development for some timewith the expectation that they will be useful for treating or preventingatherosclerosis. A number of classes of CETP inhibitor drugs have beenshown to increase HDL, decrease LDL in humans and to have therapeuticeffects for treating atherosclerosis and cardiovascular diseaseincluding dalcetrapib, torcetrapib, anacetrapib, evacetrapib, BAY60-5521 and others (Table 1).

TABLE 1 Overview of Lead CETP Inhibitor Drugs and Clinical StatusStructure Compound Clinical phase

Torcetrapib Phase III discontinued in 2006

Anacetrapib Phase III

Dalcetrapib Phase III trial halted May 2012

BAY 60-5521 Phase I

However there is evidence that these drugs may not be safe and effectivein all patients. The clinical trial for torcetrapib was terminated inPhase III due to incidence of mortality in patient to whom torcetrapiband atorvastatin were administered concomitantly compared to patientstreated with atorvastatin alone. The clinical trial for dalcetrapib wasalso halted in Phase III in this case due to a lack of efficacy relativeto statins alone. Additional CETP inhibitors are still being pursued inclinical trials and earlier stage development. In general treatmentstrategies using CETP inhibitors that provide better efficacy, reducedoff-target effects would be clinically beneficial. There is a need forbiomarkers, methods and approaches for predicting response to CETPinhibitors and accessing risk of adverse events associated withadministration of CETP inhibitors.

CETP inhibitors are useful for the treatment and/or prophylaxis ofatherosclerosis, peripheral vascular disease, dyslipidemia,hyperbetalipoproteinemia, hypoalphalipoproteinemia,hypercholesterolemia, hypertriglyceridemia, familialhypercholesterolemia, cardiovascular disorders, angina, ischemia,cardiac ischemia, stroke, myocardial infarction, reperfusion injury,angioplastic restenosis, hypertension, and vascular complications ofdiabetes, obesity or endotoxemia.

Clinical trials have shown that patient response to treatment withpharmaceuticals is often heterogeneous. There a pressing need to improvedrug development, clinical development and the therapeutic impact ofdrugs for individuals or sub-populations of patients. Single nucleotidepolymorphisms (SNPs) can be used to identify patients most suited totherapy with particular pharmaceutical agents (this is often termed“pharmacogenomics”). Similarly, SNPs can be used to exclude patientsfrom certain treatment due to the patient's increased likelihood ofdeveloping toxic side effects or their likelihood of not responding tothe treatment. Pharmacogenomics can also be used in pharmaceuticalresearch to assist the drug development and selection process. Linder etal, Clinical Chemistry 43:254 (1997); Marshall, Nature Biotechnology 15:1249 (1997); International Patent Application WO 97/40462, SpectraBiomedical; and Schafer et al, Nature Biotechnology 16:3 (1998).

The dalcetrapib mortality and morbidity trial (dal-OUTCOMES) was adouble-blind, randomized, placebo-controlled, parallel group,multi-centre study in stable CHD patients recently hospitalized foracute coronary syndrome (ACS). The study was conducted to test thehypothesis that CETP inhibition will reduce the risk of recurrentcardiovascular events in patients with recent ACS by raising levels ofHDL-C through CETP inhibition. Eligible patients entered a single-blindplacebo run-in period of approximately 4 to 6 weeks to allow forpatients to stabilize and for completion of planned revascularizationprocedures. At the end of the run-in period, eligible patients in stablecondition were randomized in a 1:1 ratio to 600 mg of dalcetrapib orplacebo on top of evidence-based medical care for ACS. Dalcetrapib is aninhibitor of cholesterol-ester transfer protein (CETP). It has beenshown to induce dose-related decreases in CETP activity and increases inHDL-C levels in several animal species and in humans. Decreasing CETPactivity, through different approaches, has demonstratedanti-atherosclerotic effects in several animal models. The trial wasinterrupted in May 2012 by the DSMB on grounds of futility. Thedal-OUTCOMES study resulted in unexpected observations related tocardiovascular disease progression. Despite a marked increase in HDL-c,patients on treatment did not show a significant reduction incardiovascular events and the study was terminated.

Following the termination of dal-OUTCOMES study, it was hypothesizedthat a subgroup of the patients under study were responding differentlyto dalcetrapib and that dalcetrapib could be having a significanttherapeutic effect in a sub-population of patients. A pharmacogenomicstudy of the dal-OUTCOMES study population was conducted to study theinter-individual variation in dalcetrapib response and to identifygenetic markers for predicting therapeutic response to dalcetrapib, orother CETP inhibitors, for patient stratification and for treatmentselection.

SUMMARY OF THE INVENTION

The present invention provides genotyping methods, reagents andcompositions for selecting individuals who can benefit from treatmentwith HDL-raising or HDL mimicking agent, in particular with a CETPinhibitor/modulator, in particular wherein the individuals havecardiovascular disorder. The invention also provides methods of treatingpatients with a cardiovascular disorder comprising genotyping andselection of patients who may benefit from treatment with HDL-raising orHDL mimicking agent, in particular with a CETP inhibitor/modulator.Surprisingly the pharmacogenomic study of the dal-OUTCOMES patientcohort found single nucleotide polymorphisms (SNPs), genetic markers,associated with an individual's response to dalcetrapib and useful forpredicting therapeutic response to HDL-raising or HDL mimicking agent(in particular a CETP inhibitor/modulator) and in treating patients withHDL-raising or HDL mimicking agent (in particular CETPinhibitor/modulator).

The invention further provides methods for treating or preventing acardiovascular disorder, comprising administering to a subject in needthereof an amount of an HDL-raising or HDL mimicking agent that iseffective to treat or prevent the cardiovascular disorder, wherein thesubject has a polymorphism at rs11647778 in the subject's ADCY9 gene. Insome embodiments, the subject has a genotype of CC at rs11647778. Incertain embodiments, the HDL-raising or HDL mimicking agent is niacin,fibrates, glitazone, dalcetrapib, anacetrapib, evacetrapib, DEZ-001,ATH-03, DRL-17822 (Dr. Reddy's), DLBS-1449, RVX-208, CSL-112, CER-001 orApoA1-Milnano.

Genetic markers detected in the genotyping methods of the inventioninclude: 20 SNPs that occur in the Adenylate Cyclase Type 9 (ADCY9) geneon chromosome 16, rs11647778 and optionally rs1967309, rs12595857,rs2239310, rs11647828, rs8049452, rs12935810, rs74702385, rs17136707,rs8061182, rs111590482, rs4786454, rs2283497, rs2531967, rs3730119,rs2531971, rs2238448, rs12599911, rs12920508, or rs13337675, inparticular rs11647778 or rs1967309, which are both in strong linkagedisequilibrium together (r²=0.79) and strongly associated with responseto an HDL-raising or HDL mimicking agent, in particular a CETPinhibitor/modulator.

Other gene markers of the invention include a SNP in the ADCY9 gene thatare either in linkage disequilibrium with rs11647778 or rs1967309 orprovided an association signal with clinical events with a statisticalP<0.05 and may provide useful surrogate biomarkers of rs11647778 orrs1967309. In one embodiment a surrogate biomarker, consisting of a SNPinherited in linkage disequilibrium with rs11647778 or rs1967309, aredetected and the genotype of rs11647778 or rs1967309 are inferred.

The present invention relates to methods of genotyping patients and/ortreating patients with HDL-raising drug, in particular a CETP inhibitor.In particular embodiments, the methods comprise assessing the genotypeof a patient at rs11647778. Three genotypes at rs11647778 are predictiveof an individual's response to an HDL-raising drug, in particular a CETPinhibitor: CC, CG and GG. Of these the CC genotype is associated with animproved therapeutic response in patients treated with an HDL-raisingdrug, the CG genotype is associated with a partial response and the GGgenotype is associated with a lack of response (non-response). For thepurpose of the present invention: patients who carry the CC genotype canbenefit from treatment with an HDL-raising drug; patients who carry theCG genotype can benefit from treatment with an HDL-raising drug andpatients who carry the GG genotype cannot benefit from treatment with anHDL-raising drug. Two genotypes at rs11647778, CC and CG indicate atherapeutic response to a CETP inhibitor, in particular dalcetrapib, inpatients with cardiovascular disorder. In particular, CC genotype forrs11647778 is indicative of greater therapeutic response to a CETPinhibitor, in particular dalcetrapib, in patients with cardiovasculardisorder.

The present invention relates to nucleic acid molecules containingpolymorphisms or gene variants, variant proteins encoded by thesenucleic acid molecules, reagents for detecting the polymorphic nucleicacid molecules, and methods of using the nucleic acid molecules andproteins as well as methods of using reagents for their detection (e.g.,primers and probes for use in the genotyping methods of the invention).

In one embodiment the invention provides: methods of detecting the genevariants of the invention and detection reagents, such as probes orprimers, for use in these methods.

The invention specifically provides, genetic markers associated withtherapeutic response to a HDL-raising or HDL mimicking agent, inparticular a CETP inhibitor/modulator, and synthetic nucleic acidmolecules (including DNA and RNA molecules) containing the gene variantsof the invention. The invention further provides variant proteinsencoded by nucleic acid molecules containing such gene variants,antibodies to the encoded variant proteins, computer-based and datastorage systems containing the novel gene variant or SNP information,methods of detecting these SNPs in a test sample, methods of identifyingindividuals who respond therapeutically when administered a HDL-raisingor HDL mimicking agent, in particular a CETP inhibitor/modulator, basedon the presence or absence of one or more of the gene variants of theinvention or the detection of one or more encoded variant products(e.g., variant mRNA transcripts or variant proteins), and methods oftreating individuals who have a cardiovascular disease who carry one ofmore of the gene variants of the invention.

Exemplary embodiments of the present invention further provide methodsfor selecting or formulating a treatment regimen (e.g., methods fordetermining whether or not to administer HDL-raising or HDL mimickingagent, in particular CETP inhibitor/modulator treatment to anindividual).

Various embodiments of the present invention also provide methods forselecting individuals to whom a HDL-raising or HDL mimicking agent (inparticular CETP inhibitor/modulator) can be therapeutically administeredbased on the individual's genotype, and methods for selectingindividuals for participation in a clinical trial of a HDL-raising orHDL mimicking agent (in particular a CETP inhibitor/modulator) based onthe genotypes of the individuals (e.g., selecting individuals toparticipate in the trial who are most likely to respond positivelyand/or excluding individuals from the trial who are unlikely to respondpositively to treatment based on their genotype(s), in particular theirgenotype is CC at rs11647778, TT at rs2238448, and/or AA at rs1967309,or selecting individuals who are unlikely to respond positively forparticipation in a clinical trial of alternative drug that may benefitthem.

The nucleic acid molecules of the invention can be inserted in anexpression vector, to produce a variant protein in a host cell. Thus,the present invention also provides for a vector comprising aSNP-containing nucleic acid molecule of the invention,genetically-engineered host cells containing the vector, and methods forexpressing a recombinant variant protein using such host cells. Inanother specific embodiment, the host cells, SNP-containing nucleic acidmolecules, and/or variant proteins can be used as targets in a methodfor screening or identifying therapeutic agents that are HDL-raising orHDL mimicking agent (in particular CETP inhibitor/modulator).

Exemplary SNPs of ADCY9 that can be determined/evaluated in the hereinprovided method for identification of an improved response todalcetrapib or for treating or preventing a cardiovascular disease in apatient are those where the mutation results in a change in thenucleotide sequence at position 4,062,592, 4,065, 583, 4,059,439 and4,051,380, (genome assembly GRCh37.p5) also known as single nucleotidepolymorphisms with identifiers rs12595857, rs1967309, rs2238448, andrs11647778, respectively, as shown in SEQ. ID. NO. 2 1, 19 and 21.

The present invention is based on the identification of geneticpolymorphisms that are predictive of an increased likelihood thattreatment with a HDL-raising or HDL mimicking agent, in particular CETPinhibitor/modulator may benefit patients with cardiovascular disorders.

DESCRIPTION OF THE DRAWINGS

FIG. 1: SNP rs1967309 is strongly associated with a reduction ofcardiovascular events (coronary heart disease death, resuscitatedcardiac arrest, non-fatal myocardial infarction, non-fatal ischemicstroke, unstable angina or unanticipated coronary revascularization) inpatients treated with the CETP inhibitor dalcetrapib. The figures showthe results of the genome-wide association study of patients from thedalcetrapib arm of the dal-OUTCOMES trial. A shows results in aManhattan plot with a strong signal in the ADCY9 gene region onchromosome 16. Each dot represents a P value for association of SNPswith minor allele frequencies >0.05 tested with Cox proportional hazardsmodel for the occurrence of cardiovascular events during treatment andadjusted for sex and 5 principal components for genetic ancestry. Bshows results for single-nucleotide polymorphisms in the ADCY9 regionalong with 6 imputed SNPs with P<10′. The x axis shows the genomiclocation of the ADCY9 gene on chromosome 16. The left y axis shows thenegative log₁₀ of P values for the comparison between cardiovascularevents versus no events weighted for imputation probability in alogistic regression model framework. The right y axis shows therecombination rate. The degree of linkage disequilibrium is presented ona grayscale gradient according to r² as estimated from the reference CEUsamples from HapMap.

FIG. 2: Frequency of cardiovascular events (dal-OUTCOMES primarycomposite event or unanticipated coronary revascularization) by studytermination in the dalcetrapib and placebo treatment arms separately andby rs1967309 genotypes in the ADCY9 gene. Percentages of events arereported with 95% CI.

FIG. 3: Cumulative incidence of cardiovascular events (dal-OUTCOMESprimary composite event or unanticipated coronary revascularization) forthe dalcetrapib treatment arm and the placebo arm separately andstratified by the three genotypes at the rs1967309 SNP in the ADCY9 gene(GG, AG, AA).

FIG. 4: Shows changes in lipid levels according to genotype during 24months of dalcetrapib treatment. Panel A. Mean±SE (mg/dL) of change oflipid values from baseline to 1 month by genotype groups of the ADCY9SNP rs1967309 for the dalcetrapib arm. P values are shown for univariatestatistics between change in lipid and genotypes. Panel B. Mean±95% CIfor absolute values of LDL-cholesterol during the follow up-period ofthe dal-Outcomes trial for patients in the dalcetrapib arm. P value formultivariate mixed regression model.

FIG. 5: Multi-dimensional scaling (MDS) plot showing the first twodimensions (C1, C2) from 76,854 SNPs for 6297 individuals from thegenetic study of dal-Outcomes and 83 CEU founder, 186 JPT-CHB and 88 YRIfounder from the 1000 genome data set. There were 436 ethnic outliersremoved from the dataset (shown with +), and dal-Outcomes samplesretained for analysis are shown.

FIG. 6: Plot of the genomic variance explained by the first tencomponents from the principal component analysis from 76,854 SNPs for6297 individuals from the genetic study of dal-Outcomes and 83 CEUfounder, 186 JPT-CHB and 88 YRI founder from the 1000 genome data set.

FIG. 7: Quantile-quantile (QQ) plot of observed −log₁₀ (P values) versusthe expectation under the null hypothesis for the genome-wideassociation of SNPs with MAF ≥0.05. The shaded region is the 95%concentration band formed by calculating the 2.5th and 97.5thpercentiles of the distribution under the null hypothesis. Dotsrepresent the ranked P values from the Cox proportional hazards modelfor time to occurrence of cardiovascular events of participants in thedalcetrapib arm and adjusted for sex and 5 principal components forgenetic ancestry. The observed genomic inflation factor was 1.01.

FIG. 8: Linkage disequilibrium of 27 genotyped SNPs in the ADCY9 geneshowing r² values, linkage disequilibrium blocks calculated using theconfidence interval method are shown in black and the D′ statistic isshown in shades of red. Linkage disequilibrium in 5686 Caucausians fromthe dal-Outcomes study.

FIG. 9: Linkage disequilibrium of 27 genotyped SNPs in the ADCY9 geneshowing r² values, linkage disequilibrium blocks calculated using theconfidence interval method are shown in black and the D′ statistic isshown in shades of red. Linkage disequilibrium in 386 participants ofthe dal-Plaque-2 study.

FIG. 10: Manhattan plot of association for genetic variants with events(primary composite endpoint) in the dal-Outcomes dalcetrapib arm, testedusing dosage data of imputed SNPs within a logistic regression frameworkwith PLINK software and adjusted for gender and 5 principal componentsfor genetic ancestry.

DETAILED DESCRIPTION OF THE INVENTION

Various features and embodiments of the present invention are disclosedherein, however other features of the invention, modifications andequivalents will be apparent to a person skilled in the relevant art,based on the teachings provided. The invention described is not limitedto the examples and embodiments provided, various alternativesequivalents will be appreciate by those skilled in the art. As usedherein, the singular forms “a”, “an” and “the” include the plural unlessthe context clearly dictates otherwise. For example, “a” cell will alsoinclude “cells”.

The term “about” when used in connection with a referenced numericindication means the referenced numeric indication plus or minus up to10% of that referenced numeric indication. For example, “about 100”means from 90 to 110.

An “allele” is defined as any one or more alternative forms of a givengene. In a diploid cell or organism the members of an allelic pair (i.e.the two alleles of a given gene) occupy corresponding positions (loci)on a pair of homologous chromosomes and if these alleles are geneticallyidentical the cell or organism is said to be “homozygous”, but ifgenetically different the cell or organism is said to be “heterozygous”with respect to the particular gene.

A “gene” is an ordered sequence of nucleotides located in a particularposition on a particular chromosome that encodes a specific functionalproduct and may include untranslated and untranscribed sequences inproximity to the coding regions. Such non-coding sequences may containregulatory sequences needed for transcription and translation of thesequence or introns etc. or may as yet to have any function attributedto them beyond the occurrence of the SNP of interest.

“genotyping” refers to the determination of the genetic information anindividual carries at one or more positions in the genome. For example,genotyping may comprise the determination of which allele or alleles anindividual carries for a single SNP or the determination of which alleleor alleles an individual carries for a plurality of SNPs. For example,at rs1967309 the nucleotides may be a A in some individuals and a G inother individuals. Those individuals who have a A at the position havethe A allele and those who have a G have the G allele. In a diploidorganism the individual will have two copies of the sequence containingthe polymorphic position so the individual may have a A allele and a Gallele or alternatively, two copies of the A alleles or two copies ofthe G allele. Those individuals who have two copies of the G allele arehomozygous for the G allele, those individuals who have two copies ofthe A allele are homozygous for the A allele, and those individuals whohave one copy of each allele are heterozygous. The alleles are oftenreferred to as the A allele, often the major allele, and the B allele,often the minor allele. The genotypes may be AA (homozygous A), BB(homozygous B) or AB (heterozygous). Genotyping methods generallyprovide for identification of the sample as AA, BB or AB.

The term “comprising” is intended to mean that the compositions andmethods include the recited elements, but do not exclude others.

“HDL-raising or HDL mimicking agent” refers to compounds which increaseHDL levels by either one of the following mechanisms: CETPinhibition/modulation, PPAR agonism, LXR agonism, HM74 agonism (niacinreceptor) thyrotropin hormone receptor agonism, Inhibitors of lipasesand HDL catabolism ApoA1 inducers, compounds which provide at least oneof the HDL athero-protective activities such as compounds that wouldincrease cellular lipid efflux (cholesterol and/or phospholipids), haveantioxidant and anti-inflammatory activities. In particular HDLmimicking agent is ApoA1 and ApoA1 derivatives (such as apoA1 Milano,ApoA1 Paris) and other analogues, reconstituted HDL containing ApoA1 andor ApoAII and the appropriate lipids such as phospholipids. ApoE,derivatives, analogues, and peptidomimetics of amphipathic lipoproteins.Examples of “HDL-raising or HDL mimicking agent” are niacin, fibrates,glitazone, dalcetrapib, anacetrapib, evacetrapib, DEZ-001 (formerlyknown as TA-8995)(Mitsubishi Tanabe Pharma), ATH-03 (Affris), DRL-17822(Dr. Reddy's), DLBS-1449 (Dexa Medica), RVX-208 (Resverlogix), CSL-112(C1s Behring), CER-001 (Cerenis), ApoA1-Milnano (Medicine Company).Particular examples of “HDL-raising or HDL mimicking agent” are niacin,fibrates, glitazone, dalcetrapib, anacetrapib, evacetrapib, torcetrapibpreferably niacin, fibrates, glitazone, dalcetrapib, anacetrapib orevacetrapib. More particularly HDL-raising or mimicking agent isselected from a CETP inhibitor/modulator. Examples of CETPinhibitor/modulators are dalcetrapib, anacetrapib, evacetrapib, DEZ-001(formerly known as TA-8995)(Mitsubishi Tanabe Pharma), ATH-03 (Affris),DRL-17822 (Dr. Reddy's), DLBS-1449 (Dexa Medica). More particularlyexamples of CETP inhibitor/modulators are dalcetrapib, anacetrapib,evacetrapib and torcetrapib, preferably dalcetrapib, anacetrapib andevacetrapib. Most particularly the HDL-raising or mimicking agentaccording to the invention would refer to a CETP inhibitor/modulator,especially when the CETP inhibitor/modulator is dalcetrapib.

“CETP inhibitor/modulator” refers to a compound which decreases CETPactivity (assessed by standard transfer assays) by inhibiting CETPand/or inducing conformational changes of the CETP polypeptide oncebound to the CETP polypeptide. The CETP conformational changes of theCETP polypeptide allow CETP activity to proceed between HDL particlesand increase its recycling/turnover bay increasing the production ofnascent pre-beta HDL formation. Preferably the CETP inhibitor/modulatorrefers to all compounds that would bind to cysteine 13 of the CETPpolypeptide. More preferably, the “CETP inhibitor/modulator” is selectedfrom S-[2-[1-(2-ethylbutyl)cyclohexylcarbonylamino]-phenyl]2-methylthiopropionate, 1-(2-Ethyl-butyl)-cyclohexanecarboxylic acid(2-mercapto-phenyl)-amide and or bis[2-[1-(2-ethylbutyl)cyclohexylcarbonylamino]phenyl] disulfide. Mostpreferably, “CETP inhibitor/modulator” isS-[2-[1-(2-ethylbutyl)cyclohexylcarbonylamino]-phenyl]2-methylthiopropionateas a prodrug or 1-(2-Ethyl-butyl)-cyclohexanecarboxylic acid(2-mercapto-phenyl)-amide as its active metabolite.

“Anacetrapib” refers to((4S,5R)-5-[3,5-bis(trifluoromethyl)phenyl]-3-{[4′-fluoro-2′-methoxy-5′-(propan-2-yl)-4-(trifluoromethyl)[1,1′-biphenyl]-2-yl]methyl}-4-methyl-I,3-oxazolidin-2-one) also knownas MK 0859, CAS 875446-37-0 or a compound of formula (X_(A)).

Anacetrapib as well as methods of making and using the compound, aredescribed in WO2006/014413, WO2006/014357, WO2007005572.

“Evacatrapib” refersTrans-4-({(5S)-5-[{[3,5-bis(trifluoromethyl)phenyl]methyl}(2-methyl-2H-tetrazol-5-yl)amino]-7,9-dimethyl-2,3,4,5-tetrahydro-1H-benzazepin-1-yl}methyl)cyclohexanecarboxylic acid also known as LY2484595, CAS1186486-62-3 or acompound of formula (X_(B))

Evacetrapib as well as methods of making and using the compound aredescribed in WO2011002696.

“Torcetrapib” refers to(2R,4S)-4-[(3,5-bistrifluoromethylbenzyl)methoxycarbonylamino]-2-ethyl-6-trifluoromethyl-3,4-dihydro-2H-quinoline-1-carboxylicacid ethyl ester, also known as CP-529,414, CAS 262352-17-0 or acompound of formula (X_(C))

Torcetrapib as well as methods of making and using the compound aredescribed in WO0017164 or WO0140190.

“BAY 60-5521” refers to (5S)-5-Quinolinol,4-cyclohexyl-2-cyclopentyl-3-[(S)-fluoro[4-(trifluoromethyl)phenyl]methyl]-5,6,7,8-tetrahydro-7,7-dimethyl-,also known as CAS 893409-49-9 or a compound of formula (XD)

BAY 60-5521 as well as methods of making and using the compound aredescribed in WO2006063828.

“Treatment” refers to both therapeutic treatment and prophylactic orpreventative measures. Those in need of treatment include those alreadywith the disorder as well as those in which the disorder is to beprevented or delayed.

The term “polymorphism” “polymorphism site” Polymorphic site” or “singlenucleotide polymorphism site” (SNP site) or “single nucleotidepolymorphism” refers to a location in the sequence of a gene whichvaries within a population. A polymorphism is the occurrence of two ormore forms of a gene or position within a gene “allele”, in apopulation, in such frequencies that the presence of the rarest of theforms cannot be explained by mutation alone. Preferred polymorphic siteshave at least two alleles. The implication is that polymorphic allelesconfer some phenotype variability on the host. Polymorphism may occur inboth the coding regions and the noncoding region of genes. Polymorphismmay occur at a single nucleotides site or may involve an insertion or adeletion. The location of such a polymorphism may be identified by itsnucleotide position in the gene, on the chromosome or on thetranscriptor by the amino acids that is altered by the nucleotidepolymorphism. Individual polymorphisms are also assigned uniqueidentifiers (“Reference SNP”, “refSNP” or “rs#”) known to one of skillin the art and used, e.g., in the Single Nucleotide PolymorphismDatabase (dbSNP) of Nucleotide Sequence Variation available on the NCBIwebsite.

The terms “linkage disequilibrium” or “in linkage disequilibrium” or“LD” refers to the non-random association of alleles in a collection ofindividuals, in other words it is the preferential segregation of aparticular polymorphic form with another polymorphic form at a differentchromosomal location more frequently than expected by chance. Byopposition the alleles that co-occur at expected frequencies are said tobe in ‘linkage equilibrium”.

The “rs” prefix refers to a SNP in the database found at the NCB1 SNPdatabase http://www.ncbi.nlm.nih.gov/snp/?term. The “rs” numbers are theNCBI rsSNP ID form.

The term “sample” includes any biological sample taken from a patient orindividual including a cell, tissue sample or body fluid. For example, asample may include a skin sample, a cheek cell sample, saliva or bloodcells. A sample can include, without limitation, a single cell, multiplecells, fragments of cells, an aliquot of a body fluid, whole blood,platelets, serum, plasma, red blood cells, white blood cells,endothelial cells, tissue biopsies, synovial fluid and lymphatic fluid.In particular “sample” refers to blood cells.

The term “therapeutic agents” refers to agents capable of treating orpreventing cardiovascular disorder. As used herein, an agent “capable oftreating or preventing cardiovascular disorder” refers to a moleculethat is capable of treating and/or preventing a cardiovascular disorderin humans and/or in a cellular or animal model of said cardiovasculardisorder.

An “improved response polymorphism”, “improved response genotype” or“responsive genotype” as used herein refers to an allelic variant orgenotype at one or more polymorphic sites within the ADCY9 gene asdescribed herein (for example, rs11647778/CC), which predicts that asubject will respond therapeutically and benefit from treatment with anHDL-raising or HDL mimicking agent (which may be measured by a decreasednumber of cardiovascular events) as compared to an allelic variant orgenotype or polymorphism (for example, rs11647778/CG or rs11647778/GG)which predicts that a subject will respond less to HDL-raising or HDLmimicking agent administration. “Reduced response” “partial response”,“non response” or “lack of therapeutic efficacy”, may be measured by arelative increase in number of cardiovascular events relative tosubjects having an “improved response genotype”. Alternately, “improvedresponse”, “responder” or “therapeutic efficacy” may be measured by arelative decrease in number of cardiovascular events relative tosubjects that carry polymorphisms associated with “non response” or“partial response” to a HDL-raising or HDL mimicking agent. Inparticular rs11647778/CC, and optionally rs12595857/GG, rs1967309/AA,rs111590482/AG, rs111590482/GG, rs11647828/GG, rs12935810/GG,rs17136707/GG, rs2239310/GG, rs2283497/AA, rs2531967/AA, rs3730119/AA,rs4786454/AA, rs74702385/GA, rs74702385/AA, rs8049452/GG, rs8061182/AAand rs2238448/TT are improved response genotypes. More particularly,rs11647778/CC and optionally rs1967309/AA, and rs2238448/TT is andimproved response genotype. Most particularly, rs11647778/CC andrs1967309/AA is improved response genotype.

“Cardiovascular events” as used herein refers to cardiovascular death,non-fatal myocardial infarction (MI), non-fatal stroke of ischemicorigin, hospitalization for unstable angina and coronaryrevascularization.

“Oligonucleotides” as used herein are variable length nucleic acids orpolynucleotides. Such oligonucleotides may be useful as probes, primersand in the manufacture of microarrays (arrays) for the detection and/oramplification of specific nucleic acids. Such DNA or RNA strands may besynthesized by the sequential addition (5′-3′ or 3 ‘-5’) of activatedmonomers to a growing chain, which may be linked to an insolublesupport. Numerous methods are known in the art for synthesizingoligonucleotides for subsequent individual use or as a part of theinsoluble support, for example in arrays (BERNFIELD M R. and ROTTMAN FM. J. Biol. Chem. (1967) 242(18):4134-43; SULSTON J. et al. PNAS (1968)60(2):409-415; GILLAM S. et al. Nucleic Acid Res. (1975) 2(5):613-624;BONORA G M. et al. Nucleic Acid Res. (1990) 18(11):3155-9; LASHKARI D A.et al. PNAS (1995) 92(17):7912-5; MCGALL G. et al. PNAS (1996) 93(24):13555-60; ALBERT T J. et al. Nucleic Acid Res. (2003) 31(7):e35; GAO X.et al. Biopolymers (2004) 73(5):579-96; and MOORCROFT M J. et al.Nucleic Acid Res. (2005) 33(8):e75). In general, oligonucleotides aresynthesized through the stepwise addition of activated and protectedmonomers under a variety of conditions depending on the method beingused. Subsequently, specific protecting groups may be removed to allowfor further elongation and subsequently and once synthesis is completeall the protecting groups may be removed and the oligonucleotidesremoved from their solid supports for purification of the completechains if so desired.

The term “genotype” refers to the genetic constitution of an organism,usually in respect to one gene or a few genes or a region of a generelevant to a particular context (i.e. the genetic loci responsible fora particular phenotype). In particular, the specific combination ofalleles at a given position in a gene, such as for example, thegenotypes AA, AG, or GG which are possible genotypes of the rs1967309SNP.

A “phenotype” is defined as the observable characters of an organism.Tables 2, 3, 4 and 5 show a genotype correlation for ADCY9 SNP withvalues representing an indication of responsiveness to treatment ofcardiovascular disorders with a HDL-raising or HDL mimicking agent.

The term “biomarker” as used herein refers to a sequence characteristicof a particular variant allele (polymorphic site, such as a SNP) orwild-type allele. Biomarker also refers to a peptide or epitope encodedby a particular variant or wild-type allele.

The term “surrogate marker” as used herein refers to a genetic variant,including a SNP, that is present in linkage disequilibrium with animproved response genotype of the invention, in particularrs11647778/CC.

The term “genetic marker” as used herein refers to variants ofpolymorphic sites of a particular gene that are associated with responseto a HDL-raising or HDL mimicking agent, in particular CETPinhibitor/modulator. In particular ‘genetic marker’ as used hereinrefers to variants of polymorphic sites in the ADCY9 gene that areassociated with response to a HDL-raising or HDL mimicking agent, inparticular a CETP inhibitor/modulator.

Three genotypes at rs11647778 are predictive of an individual's responseto an HDL-raising drug, in particular a CETP inhibitor: CC, CG and GG.Of these, the CC genotype is associated with an improved therapeuticresponse in patients to an HDL-raising drug, the CG genotype isassociated with a partial response, and the GG genotype is associatedwith a lack of response (non-response). For the purpose of the presentinvention: patients who carry the CC genotype can benefit from treatmentwith an HDL-raising drug; patients who carry the CG genotype can benefitfrom treatment with an HDL-raising drug, and patients who carry the GGgenotype cannot benefit from treatment with an HDL-raising drug. The CCand CG genotypes at rs11647778 in patients with a cardiovasculardisorder indicate a therapeutic response to a CETP inhibitor, inparticular dalcetrapib. In particular, the CC genotype at rs11647778 inpatients with a cardiovascular disorder is indicative of a greatertherapeutic response to a CETP inhibitor, in particular dalcetrapib.

Three genotypes at rs2238448 are predictive of an individual's responseto an HDL-raising drug, in particular a CETP inhibitor: TT, TC and CC.Of these three genotypes, the TT genotype is associated with an improvedtherapeutic response in patients treated with an HDL-raising drug,whereas the CC genotype is associated with a lack of response(non-response). Patients who carry the TC genotype can benefit fromtreatment with an HDL-raising drug as this genotype is associated with apartial response. For the purpose of the present invention: patients whocarry the TT or CT genotype can benefit from treatment with anHDL-raising drug and patients who carry the CC genotype cannot benefitfrom treatment with an HDL-raising drug. The TT genotype at rs2238448 inpatients with a cardiovascular disorder indicates a greater therapeuticresponse to a CETP inhibitor, in particular dalcetrapib, as compared toother genotypes.

In certain methods described herein one or more biomarkers are used toidentify or select individuals who will benefit from treatment with aHDL-raising or HDL mimicking agent, in particular a CETPinhibitor/modulator. A SNP biomarker for use in the invention can bepredictive of either a therapeutic response (R) to treatment ornon-response to treatment (NR). Table 2 shows genotypes observed in thedal-Outcomes cohort, present at the polymorphic site rs1967309, whichcan be used as a biomarker to predict response to dalcetrapib orHDL-raising or HDL mimicking agent, in particular to other CETPinhibitor/modulator. Table 4 shows genotypes observed in thedal-Outcomes and dal-Plaque-2 cohorts, present at the polymorphic siters11647778, which can be used as a biomarker to predict response todalcetrapib or HDL-raising or HDL mimicking agent, in particular toother CETP inhibitor/modulator. Each genotype shown in Table 2, to 5alone or in combination with genotypes at other polymorphic sites can beused as a biomarker for predicting response to a HDL-raising or HDLmimicking agent, in particular to a CETP inhibitor/modulator).

TABLE 2 genetic markers and predicted response to treatment withHDL-raising or HDL mimicking agent SNP Genotype Responsiveness totreatment rs1967309 AA R rs1967309 AG PR rs1967309 GG NR R: ResponsivePR: Partial Responsive NR: Non Responsive

TABLE 3 genetic markers and predicted response to treatment withHDL-raising or HDL mimicking agent SNP Genotype Responsiveness totreatment rs12595857 AA NR rs12595857 AG PR rs12595857 GG R R:Responsive PR: Partial Responsive NR: Non Responsive

TABLE 4 genetic markers and predicted response to treatment withHDL-raising or HDL mimicking agent SNP Genotype Responsiveness totreatment rs11647778 GG NR rs11647778 CG PR rs11647778 CC R R:Responsive PR: Partial Responsive NR: Non Responsive

TABLE 5 genetic markers and predicted response to treatment withHDL-raising or HDL mimicking agent Responsiveness SNP Genotype toTreatment rs2238448  TT R TC PR CC NR rs111590482 AA NR AG R GG Rrs11647828  AA NR AG PR GG R rs12935810  GG R GA NR AA NR rs13337675  AANR AG PR GG PR rs17136707  AA NR AG PR GG R rs2239310  AA NR AG PR GG Rrs2283497  CC NR CA PR AA R rs2531967  GG NR GA PR AA R rs3730119  GG NRGA PR AA R rs4786454  GG NR GA PR AA R rs74702385  GG NR GA R AA Rrs8049452  GG R GA PR AA NR rs8061182  AA R AG PR GG NR R: ResponsivePR: Partial Responsive NR: Non Responsive

Rs11647778, rs1967309 and rs12595857 are located in an intronic(non-coding) region of the ADCY9 gene in a region that is concordantwith having regulatory activity on the ADCY9 gene expression.

In certain methods described herein individuals who will respondtherapeutically to treatment with a HDL-raising or HDL mimicking agent,in particular with a CETP inhibitor/modulator are identified andselected for treatment using the genotyping methods of the invention. Inparticular patients who carry rs11647778/CC and optionally one or moreof the following improved response genotypes, are selected for treatmentin the methods of the invention: rs12595857/GG, rs1967309/AA,rs111590482/AG, rs111590482/GG, rs11647828/GG, rs12935810/GG,rs17136707/GG, rs2239310/GG, rs2283497/AA, rs2531967/AA, rs3730119/AA,rs4786454/AA, rs74702385/GA, rs74702385/AA, rs8049452/GG, rs8061182/AA,rs2238448/TT. More particularly, patients who carry rs11647778/CC andoptionally rs12595857/GG, rs2238448/TT and/or rs1967309/AA genotypes areselected for treatment in the methods of the invention: Mostparticularly, patients who carry rs11647778/CC and rs1967309/AAgenotypes are selected for treatment in the methods of the invention.

In another embodiment the invention provides, a method for identifying asubject benefiting from a HDL-raising or HDL mimicking agent, the methodcomprising determining a genotype of said subject (e.g., genotyping) atone or more of polymorphic sites in the ADCY9 gene.

In another embodiment the invention provides, a method for determiningan individual's responsiveness to a HDL-raising or HDL mimicking agent,in particular a CETP inhibitor, the method comprising determining agenotype of said subject (e.g., genotyping) at rs11647778 and optionallyat one or more of rs1967309, rs12595857, rs2239310, rs11647828,rs8049452, rs12935810, rs74702385, rs17136707, rs8061182, rs111590482,rs4786454, rs2283497, rs2531967, rs3730119, rs13337675, rs12920508,rs12599911, rs2531971 or rs2238448, using one or more of the primers orprobes disclosed herein.

In another embodiment the invention provides, a method for determiningan individual's responsiveness to a HDL-raising or HDL mimicking agent,in particular a CETP inhibitor, the method comprising determining agenotype of said subject (e.g., genotyping) at rs11647778 and optionallyat one or more of rs1967309, rs12595857, rs2239310, rs11647828,rs8049452, rs12935810, rs74702385, rs17136707, rs8061182, rs111590482,rs4786454, rs2283497, rs2531967 or rs3730119, rs13337675, using one ormore of the primers or probes disclosed herein.

In a particular embodiment, the invention provides the method hereindescribed wherein the polymorphic sites comprise rs11647778 andoptionally one or more of the following sites selected from the groupconsisting of: rs1967309, rs12595857, rs2239310, rs11647828, rs8049452,rs12935810, rs74702385, rs17136707, rs8061182, rs111590482, rs4786454,rs2283497, rs2531967, rs3730119, rs13337675, rs12920508, rs12599911,rs2531971 or rs2238448, particularly wherein the polymorphic site isselected from the group consisting of rs2239310, rs11647828, rs8049452,rs12935810, rs74702385, rs17136707, rs8061182, rs111590482, rs4786454,rs2283497, rs2531967, rs3730119 and rs13337675, more particularlywherein the polymorphic site is rs11647778 and optionally rs1967309 orrs12595857, more particularly wherein the polymorphic site is rs11647778and optionally rs1967309, in particular wherein the correspondinggenotypes comprises CC and AA respectively.

In a particular embodiment, the invention provides methods of genotypingone or more polymorphic sites, wherein at least one polymorphic site isrs11647778 and optionally one or more polymorphic sites selected fromthe group consisting of: rs1967309, rs12595857, rs2239310, rs11647828,rs8049452, rs12935810, rs74702385, rs17136707, rs8061182, rs111590482,rs4786454, rs2283497, rs2531967, rs3730119, rs13337675, rs12920508,rs12599911, rs2531971 or rs2238448, particularly wherein the optionallypolymorphic site is elected from the group consisting of rs2239310,rs11647828, rs8049452, rs12935810, rs74702385, rs17136707, rs8061182,rs111590482, rs4786454, rs2283497, rs2531967, rs3730119 and rs13337675more particularly wherein the optional polymorphic site is rs1967309 or,rs12595857, more particularly wherein the optional polymorphic site isrs1967309.

In a particular embodiment, the invention provides a method wherein asubject carrying rs11647778/CC and optionally one or more ofrs12595857/GG, rs1967309/AA, rs111590482/AG, rs111590482/GG,rs11647828/GG, rs12935810/GG, rs17136707/GG, rs2239310/GG, rs2283497/AA,rs2531967/AA, rs3730119/AA, rs4786454/AA, rs74702385/GA, rs74702385/AA,rs8049452/GG, rs8061182/AA, or rs2238448/TT benefits from treatment withan HDL-raising or HDL mimicking agent, particularly wherein theHDL-raising or HDL mimicking agent is a CETP inhibitor/modulator, andmore particularly wherein the HDL-raising or HDL mimicking agent isS-(2-{[1-(2-ethyl-butyl)-cyclohexanecarbonyl]-amino}-phenyl) ester. In aparticular embodiment, the invention provides the method wherein aHDL-raising or HDL mimicking agent is administered to said subject.

In a particular embodiment, the invention provides a method wherein asubject carrying rs11647778/CC and optionally one or more ofrs12595857/GG, rs1967309/AA, rs111590482/AG, rs111590482/GG,rs11647828/GG, rs12935810/GG, rs17136707/GG, rs2239310/GG, rs2283497/AA,rs2531967/AA, rs3730119/AA, rs4786454/AA, rs74702385/GA, rs74702385/AA,rs8049452/GG, rs8061182/AA, or rs2238448/TT is treated with anHDL-raising or HDL mimicking agent, particularly wherein the HDL-raisingor HDL mimicking agent is a CETP inhibitor/modulator, and moreparticularly wherein the HDL-raising or HDL mimicking agent isS-(2-{[1-(2-ethyl-butyl)-cyclohexanecarbonyl]-amino}-phenyl) ester.

In a particular embodiment, the invention provides a method wherein asubject carrying rs11647778/CC and optionally one or more ofrs12595857/GG, rs1967309/AA, rs111590482/AG, rs111590482/GG,rs11647828/GG, rs12935810/GG, rs17136707/GG, rs2239310/GG, rs2283497/AA,rs2531967/AA, rs3730119/AA, rs4786454/AA, rs74702385/GA, rs74702385/AA,rs8049452/GG, rs8061182/AA, or rs2238448/TT is administered with anHDL-raising or HDL mimicking agent, particularly wherein the HDL-raisingor HDL mimicking agent is a CETP inhibitor/modulator, and moreparticularly wherein the HDL-raising or HDL mimicking agent isS-(2-{[1-(2-ethyl-butyl)-cyclohexanecarbonyl]-amino}-phenyl) ester.

In particular embodiments, the invention provides a method wherein thesubject, has a cardiovascular disorder, in particular wherein thecardiovascular disorder is selected from the group consisting ofatherosclerosis, peripheral vascular disease, dyslipidemia,hyperbetalipoproteinemia, hypoalphalipoproteinemia,hypercholesterolemia, hypertriglyceridemia,familial-hypercholesterolemia, angina, ischemia, cardiac ischemia,stroke, myocardial infarction, reperfusion injury, angioplasticrestenosis, hypertension, and vascular complications of diabetes,obesity or endotoxemia in a mammal, more particularly wherein thecardiovascular disorder is selected from the group consisting ofcardiovascular disease, coronary heart disease, coronary artery disease,hypoalphalipoproteinemia, hyperbetalipoproteinemia,hypercholesterolemia, hyperlipidemia, atherosclerosis, hypertension,hypertriglyceridemia, hyperlipidoproteinemia, peripheral vasculardisease, angina, ischemia, and myocardial infarction.

In another embodiment the invention provides a method of treating orpreventing a cardiovascular disorder in a subject in need thereof, themethod comprising:

-   -   (a) selecting a subject having an improved response genotype at        rs11647778 and optionally at one or more of the following sites:        rs1967309, rs12595857, rs2239310, rs11647828, rs8049452,        rs12935810, rs74702385, rs17136707, rs8061182, rs111590482,        rs4786454, rs2283497, rs2531967, rs3730119, rs13337675,        rs12920508, rs12599911, rs2531971 or rs2238448;    -   (b) administering to said subject a HDL-raising or HDL mimicking        agent, in particular a CETP inhibitor/modulator.

In another embodiment the invention provides a method of treating orpreventing a cardiovascular disorder in a subject in need thereof, themethod comprising:

-   -   (a) selecting a subject having an improved response genotype at        rs11647778 and optionally one or more of the following sites:        rs1967309, rs12595857, rs2239310, rs11647828, rs8049452,        rs12935810, rs74702385, rs17136707, rs8061182, rs111590482,        rs4786454, rs2283497, rs2531967, rs3730119, rs13337675;    -   (b) administering to said subject a HDL-raising or HDL mimicking        agent, in particular a CETP inhibitor/modulator.

In a particular embodiment the invention provides a method of treating acardiovascular disorder in a subject in need thereof, the methodcomprising:

-   -   (a) selecting a subject having an improved response polymorphism        at rs11647778 and optionally rs1967309 and/or rs2238448, in        particular wherein the subject has CC genotype at rs11647778 AA        genotype at rs1967309 and TT genotype at rs2238448;    -   (b) administering to said subject a HDL-raising or HDL mimicking        agent, in particular a CETP inhibitor/modulator.

In a particular embodiment the invention provides a method of treatingor preventing a cardiovascular disorder in a subject in need thereof,the method comprising:

-   -   (a) selecting a subject having an improved response polymorphism        at rs11647778 and optionally rs1967309, in particular wherein        the subject has CC genotype at rs11647778 and AA genotype at        rs1967309;    -   (b) administering to said subject a HDL-raising or HDL mimicking        agent, in particular a CETP inhibitor/modulator.

In another embodiment the invention provides a method of treating orpreventing a cardiovascular disorder in a subject in need thereof, themethod comprising:

-   -   (a) genotyping a subject at rs11647778 and optionally at one or        more of the following sites: rs1967309, rs12595857, rs2239310,        rs11647828, rs8049452, rs12935810, rs74702385, rs17136707,        rs8061182, rs111590482, rs4786454, rs2283497, rs2531967,        rs3730119, rs13337675, rs12920508, rs12599911, rs2531971 or        rs2238448;    -   (b) administering to said subject a HDL-raising or HDL mimicking        agent, in particular a CETP inhibitor/modulator.

In another embodiment the invention provides a method of treating orpreventing a cardiovascular disorder in a subject in need thereof, themethod comprising:

-   -   (a) genotyping a subject at rs11647778 and optionally one or        more of the following sites: rs1967309, rs12595857, rs2239310,        rs11647828, rs8049452, rs12935810, rs74702385, rs17136707,        rs8061182, rs111590482, rs4786454, rs2283497, rs2531967,        rs3730119, rs13337675;    -   (b) administering to said subject a HDL-raising or HDL mimicking        agent, in particular a CETP inhibitor/modulator.

The invention also provides a method of treating or preventing a patientcomprising:

-   -   a. analyzing a patient sample for the presence of genetic marker        rs11647778/CC and optionally one or more genetic markers        selected from the group consisting of rs12595857/GG,        rs1967309/AA, rs111590482/AG, rs111590482/GG, rs11647828/GG,        rs12935810/GG, rs17136707/GG, rs2239310/GG, rs2283497/AA,        rs2531967/AA, rs3730119/AA, rs4786454/AA, rs74702385/GA,        rs74702385/AA, rs8049452/GG and rs8061182/AA and    -   b. administering to a patient who carries one or more of said        genetic markers with a HDL-raising or HDL mimicking agent, in        particular a CETP inhibitor/modulator.

The invention also provides a method of treating a patient comprising:

-   -   a. analyzing a patient sample for the presence of genetic marker        rs11647778/CC and optionally one or more genetic markers        selected from the group consisting of rs12595857/GG,        rs1967309/AA, rs111590482/AG, rs111590482/GG, rs11647828/GG,        rs12935810/GG, rs17136707/GG, rs2239310/GG, rs2283497/AA,        rs2531967/AA, rs3730119/AA, rs4786454/AA, rs74702385/GA,        rs74702385/AA, rs8049452/GG and rs8061182/AA and    -   b. treating a patient who carries one or more of said genetic        markers with a HDL-raising or HDL mimicking agent, in particular        a CETP inhibitor/modulator.

In a particular embodiment, the invention provides the method wherein agenotype is determined at rs11647778 and optionally one or more sitesselected from: rs1967309 and rs12595857.

In a particular embodiment, the present invention provides a method ofdetermining individuals responsiveness to a HDL-raising drug comprising:

-   -   a. obtaining a sample from the individual, wherein the sample        comprising genetic material;    -   b. contacting the sample with a reagent, such as probes or        primers, generating a complex between the reagent and a genetic        marker selected from Table 10;    -   c. detecting the complex to obtain a dataset associated with the        sample and    -   d. analyzing the dataset to determine the presence or absence of        a genetic marker.

In a particular embodiment, the present invention provides a method ofdetermining responsiveness to an HDL-raising drug in a patient havingone or more symptoms of a cardiovascular disease comprising:

-   -   a. obtaining a sample from the patient, wherein the sample        comprises genetic material;    -   b. contacting the genetic material with a reagent, such as a        probe or primer set to generate a complex between the reagent        and a genetic marker selected from Table 10;    -   c. detecting the complex to obtain a dataset associated with the        sample;    -   d. analyzing the dataset to determine the presence or absence of        a genetic marker; and    -   e. identifying a patient who has one or more genetic markers as        a candidate to receive an HDL-raising drug.

The complex between the reagent (such as probes or primers) and agenetic marker generated in the genotyping methods provided can begenerated by either polymerase chain reaction (PCR) or DNA sequencing.Such methods are described herein and are well known to those of skillin the art.

The invention provides reagents (such as probes or primers) forgenotyping a genetic marker selected from rs11647778/CC, rs12595857/GG;rs1967309/AA; rs111590482/AG; rs111590482/GG; rs11647828/GG;rs12935810/GG; rs17136707/GG; rs2239310/GG; rs2283497/AA; rs2531967/AA;rs3730119/AA; rs4786454/AA; rs74702385/GA; rs74702385/AA; rs8049452/GG;rs11647778/CG, rs8061182/AA; rs1967309/GA, rs12595857/AG, rs13337675/AG,rs13337675/GG, rs17136707/AG, rs2239310/AG, rs2283497/CA, rs2531967/GA,rs3730119/GA, rs4786454/GA, rs8049452/GA, rs8061182/AG, rs12595857/GG,rs1967309/AA, rs111590482/AG, rs111590482/GG, rs11647828/GG,rs12935810/GG, rs17136707/GG, rs2239310/GG, rs2283497/AA, rs2531967/AA,rs3730119/AA, rs4786454/AA, rs74702385/GA, rs74702385/AA, rs8049452/GG,rs8061182/AA, rs12935810/GA, rs12935810/AA, rs11647828/AA, rs2531967/GG,rs3730119/GG, rs2239310/AA, rs12595857/AA, rs111590482/AA,rs74702385/GG, rs11647778/GG, rs1967309/GG, rs2283497/CC, rs8061182/GG,rs17136707/AA, rs2238448/TT, rs2238448/TC, rs2238448/CC, rs8049452/AA,rs4786454/GG, rs13337675/AA and rs11647828/AG, preferably rs11647778, inparticular a primer or a probe.

In a particular embodiment, the primer comprises strand of DNA that is15 to 30 nucleotides in length and hybridizes under high stringencyconditions to a region of chromosome 16 adjacent to rs11647778,rs1967309, rs12595857, rs2239310, rs11647828, rs8049452, rs12935810,rs74702385, rs17136707, rs8061182, rs111590482, rs4786454, rs2283497,rs2531967, rs3730119, rs13337675, rs12920508, rs12599911, rs2531971 orrs2238448.

In a particular embodiment the primer comprises a strand of DNA that is15 to 30 nucleotides in length and hybridizes under high stringencyconditions to a region of chromosome 16 adjacent to rs11647778.

In a particular embodiment, the primer comprises a strand of DNA that is15 to 30 nucleotides in length and hybridizes under high stringencyconditions to a region of chromosome 16 adjacent to rs11647778,rs1967309, rs12595857, rs2239310, rs11647828, rs8049452, rs12935810,rs74702385, rs17136707, rs8061182, rs111590482, rs4786454, rs2283497,rs2531967, rs3730119, rs2238448 or rs13337675.

In a particular embodiment, the primer comprises strand of DNA that is15 to 30 nucleotides in length and hybridizes under high stringencyconditions to a region of chromosome 16 adjacent to rs11647778.

In another embodiment, the reagent is a primer comprising a strand ofDNA that is 15 to 30 nucleotides in length and hybridizes under highstringency conditions to a region of chromosome 16 overlapping withrs11647778, rs1967309, rs12595857, rs2239310, rs11647828, rs8049452,rs12935810, rs74702385, rs17136707, rs8061182, rs111590482, rs4786454,rs2283497, rs2531967, rs3730119, rs13337675, rs12920508, rs12599911,rs2531971 or rs2238448.

In another embodiment the reagent is a primer comprising a strand of DNAthat is 15 to 30 nucleotides in length and hybridizes under highstringency conditions to a region of chromosome 16 overlapping withrs11647778.

In another embodiment the reagent is a primer a comprising strand of DNAthat is 15 to 30 nucleotides in length and hybridizes under highstringency conditions to a region of chromosome 16 overlapping withrs11647778, rs1967309, rs12595857, rs2239310, rs11647828, rs8049452,rs12935810, rs74702385, rs17136707, rs8061182, rs111590482, rs4786454,rs2283497, rs2531967, rs3730119, rs2238448 or rs13337675.

In another embodiment the reagent is a primer comprising a strand of DNAthat is 15 to 30 nucleotides in length and hybridizes under highstringency conditions to a region of chromosome 16 overlapping withrs11647778.

In another embodiment the probe is a nucleic acid that is 15 to 30nucleotides in length and hybridizes under high stringency conditions toa region of chromosome 16 overlapping with rs11647778, rs1967309,rs12595857, rs2239310, rs11647828, rs8049452, rs12935810, rs74702385,rs17136707, rs8061182, rs111590482, rs4786454, rs2283497, rs2531967,rs3730119, rs13337675, rs12920508, rs12599911, rs2531971 or rs2238448.

In another embodiment the probe is a nucleic acid that is 15 to 30nucleotides in length and hybridizes under high stringency conditions toa region of chromosome 16 overlapping with rs11647778.

In another embodiment the probe is a nucleic acid that is 15 to 30nucleotides in length and hybridizes under high stringency conditions toa region of chromosome 16 overlapping with rs11647778, rs1967309,rs12595857, rs2239310, rs11647828, rs8049452, rs12935810, rs74702385,rs17136707, rs8061182, rs111590482, rs4786454, rs2283497, rs2531967,rs3730119, rs2238448 or rs13337675.

In another embodiment the probe is a nucleic acid that is 15 to 30nucleotides in length and hybridizes under high stringency conditions toa region of chromosome 16 overlapping with rs11647778.

In another embodiment the probe is a nucleic acid that is 15 to 30nucleotides in length and hybridizes under high stringency conditions toan oligonucleotide selected from SEQ. ID. NO. 1 to SEQ. ID. NO 21.

In another embodiment the probe is a nucleic acid that is 15 to 30nucleotides in length and hybridizes under high stringency conditions toan oligonucleotide having the sequence of SEQ. ID NO 21.

In another embodiment, the probe is a nucleic acid that is 15 to 30nucleotides in length and hybridizes under high stringency conditions toan oligonucleotide having the sequence of SEQ. ID NO. 19.

In a particular embodiment, the invention provides the method whereinthe HDL-raising or HDL mimicking agents a CETP inhibitor/modulator, inparticular, wherein the HDL-raising or HDL mimicking agent isS-(2-{[1-(2-ethyl-butyl)-cyclohexanecarbonyl]-amino}-phenyl) ester.

In yet another embodiment, the invention provides a use of HDL-raisingor HDL mimicking agent, in particular a CETP inhibitor/modulator, in themanufacture of a medicament for the treatment or prevention of acardiovascular disorder in a subject in need thereof, wherein thesubject has an improved response genotype at rs11647778 and optionallyone or more of the following sites: rs1967309, rs12595857, rs2239310,rs11647828, rs8049452, rs12935810, rs74702385, rs17136707, rs8061182,rs111590482, rs4786454, rs2283497, rs2531967, rs3730119, rs2238448, orrs13337675.

In a particular embodiment, the invention provides the use as definedherein, wherein the subject has an improved response polymorphism atrs11647778.

In another embodiment, the invention provides a HDL-raising or HDLmimicking agent, in particular a CETP inhibitor/modulator for use in thetreatment or prevention of a cardiovascular disorder in a subject inneed thereof, wherein the subjects carries genetic marker rs11647778/CCand optionally one or more genetic markers selected from: rs12595857/GG;rs1967309/AA; rs111590482/AG; rs111590482/GG; rs11647828/GG;rs12935810/GG; rs17136707/GG; rs2239310/GG; rs2283497/AA; rs2531967/AA;rs3730119/AA; rs4786454/AA; rs74702385/GA; rs74702385/AA; rs8049452/GG;rs8061182/AA; rs1967309/GA, rs12595857/AG, rs13337675/AG, rs13337675/GG,rs17136707/AG, rs2239310/AG, rs2283497/CA, rs2531967/GA, rs3730119/GA,rs4786454/GA, rs8049452/GA, rs8061182/AG, rs12595857/GG, rs1967309/AA,rs111590482/AG, rs111590482/GG, rs11647828/GG, rs12935810/GG,rs17136707/GG, rs2239310/GG, rs2283497/AA, rs2531967/AA, rs3730119/AA,rs4786454/AA, rs74702385/GA, rs74702385/AA, rs8049452/GG, rs8061182/AA,rs12935810/GA, rs12935810/AA, rs11647828/AA, rs2531967/GG, rs3730119/GG,rs2239310/AA, rs12595857/AA, rs111590482/AA, rs74702385/GG,rs1967309/GG, rs2283497/CC, rs8061182/GG, rs17136707/AA, rs8049452/AA,rs4786454/GG, rs13337675/AA, rs2238448/TT, and rs11647828/AG.

In another embodiment, the invention provides methods for treating orpreventing a cardiovascular disorder, comprising administering to asubject in need thereof a therapeutically effective amount of aHDL-raising or HDL mimicking agent, in particular a CETPinhibitor/modulator, wherein the subject has an improved responsegenotype at rs11647778 and optionally at one or more of the followingsites: rs1967309, rs12595857, rs2239310, rs11647828, rs8049452,rs12935810, rs74702385, rs17136707, rs8061182, rs111590482, rs4786454,rs2283497, rs2531967, rs3730119 rs2238448, and rs13337675.

In another embodiment, the invention provides methods for treating orpreventing a cardiovascular disorder, comprising administering to asubject in need thereof an amount of a HDL-raising or HDL mimickingagent, in particular a CETP inhibitor/modulator, that is effective fortreating or preventing the cardiovascular disorder, wherein the subjecthas an improved response genotype at rs11647778 and optionally at one ormore of the following sites: rs1967309, rs12595857, rs2239310,rs11647828, rs8049452, rs12935810, rs74702385, rs17136707, rs8061182,rs111590482, rs4786454, rs2283497, rs2531967, rs3730119, rs2238448, andrs13337675.

In another embodiment, the invention provides a method for treating orpreventing a cardiovascular disorder, comprising administering to asubject having an improved response genotype at rs11647778 andoptionally at one or more of the following sites: rs1967309, rs12595857,rs2239310, rs11647828, rs8049452, rs12935810, rs74702385, rs17136707,rs8061182, rs111590482, rs4786454, rs2283497, rs2531967, rs3730119,rs13337675, rs2238448a therapeutically effective amount of a HDL-raisingor HDL mimicking agent, in particular a CETP inhibitor/modulator.

In another embodiment, the invention provides a method for treating orpreventing a cardiovascular disorder, comprising administering to asubject having an improved response genotype at rs11647778 andoptionally at one or more of the following sites: rs1967309, rs12595857,rs2239310, rs11647828, rs8049452, rs12935810, rs74702385, rs17136707,rs8061182, rs111590482, rs4786454, rs2283497, rs2531967, rs3730119,rs13337675, rs2238448 an amount of an HDL-raising or HDL mimickingagent, in particular a CETP inhibitor/modulator that is effective fortreating or preventing the cardiovascular disorder.

In a particular embodiment, the invention provides method for treating acardiovascular disorder, comprising administering to a patient in needthereof a therapeutically effective amount of a HDL-raising or HDLmimicking agent, in particular a CETP inhibitor/modulator, wherein thesubjects treated have an improved response genotype, wherein thegenotype is rs11647778/CC and optionally rs12595857/GG, rs1967309/AA,rs111590482/AG, rs111590482/GG, rs11647828/GG, rs12935810/GG,rs17136707/GG, rs2239310/GG, rs2283497/AA, rs2531967/AA, rs3730119/AA,rs4786454/AA, rs74702385/GA, rs74702385/AA, rs8049452/GG and orrs8061182/AA.

In a particular embodiment, the invention provides methods for treatingor preventing a cardiovascular disorder, comprising administering to asubject in need thereof an amount of an HDL-raising or HDL mimickingagent, in particular a CETP inhibitor/modulator, that is effective fortreating or preventing the cardiovascular disorder, wherein the subjectcarries the genotype rs11647778/CC and optionally rs12595857/GG,rs1967309/AA, rs111590482/AG, rs111590482/GG, rs11647828/GG,rs12935810/GG, rs17136707/GG, rs2239310/GG, rs2283497/AA, rs2531967/AA,rs3730119/AA, rs4786454/AA, rs74702385/GA, rs74702385/AA, rs8049452/GG,rs2238448/TT, and/or rs8061182/AA.

In another embodiment, the invention provides a method for treating orpreventing a cardiovascular disorder, comprising administering to asubject having an improved response genotype at rs11647778/CC andoptionally rs12595857/GG, rs1967309/AA, rs111590482/AG, rs111590482/GG,rs11647828/GG, rs12935810/GG, rs17136707/GG, rs2239310/GG, rs2283497/AA,rs2531967/AA, rs3730119/AA, rs4786454/AA, rs74702385/GA, rs74702385/AA,rs8049452/GG and or rs8061182/AA, a therapeutically effective amount ofa HDL-raising or HDL mimicking agent, in particular a CETPinhibitor/modulator.

In another embodiment, the invention provides a method for treating orpreventing a cardiovascular disorder, comprising administering to asubject having the genotype rs11647778/CC and optionally rs12595857/GG,rs1967309/AA, rs111590482/AG, rs111590482/GG, rs11647828/GG,rs12935810/GG, rs17136707/GG, rs2239310/GG, rs2283497/AA, rs2531967/AA,rs3730119/AA, rs4786454/AA, rs74702385/GA, rs74702385/AA, rs8049452/GG,rs2238448/TT, and/or rs8061182/AA, an amount of an HDL-raising or HDLmimicking agent, in particular a CETP inhibitor/modulator that iseffective for treating or preventing the cardiovascular disorder.

In another embodiment, the invention provides a method for treating orpreventing a cardiovascular disorder, comprising administering to asubject in need thereof a therapeutically effective amount of aHDL-raising or HDL mimicking agent, in particular a CETPinhibitor/modulator, wherein the subjects treated have an improvedresponse genotype at rs11647778 and optionally rs1967309, rs2238448 orrs12595857.

In another embodiment, the invention provides a method for treating orpreventing a cardiovascular disorder, comprising administering to asubject in need thereof an amount of an HDL-raising or HDL mimickingagent, in particular a CETP inhibitor/modulator, that is effective fortreating or preventing the cardiovascular disorder, wherein the subjecthas an improved response genotype at rs11647778 and optionallyrs1967309, rs2238448, or rs12595857.

In another embodiment, the invention provides a method for treating orpreventing a cardiovascular disorder, comprising administering to asubject having an improved response genotype at rs11647778 andoptionally rs1967309, rs2238448 or rs12595857, a therapeuticallyeffective amount of a HDL-raising or HDL mimicking agent, in particulara CETP inhibitor/modulator.

In another embodiment, the invention provides a method for treating orpreventing a cardiovascular disorder, comprising administering to asubject having an improved response genotype at rs11647778 andoptionally rs1967309, rs2238448, or rs12595857, an amount of anHDL-raising or HDL mimicking agent, in particular a CETPinhibitor/modulator that is effective for treating or preventing thecardiovascular disorder.

In another embodiment, the invention provides a method for treating orpreventing a cardiovascular disorder, comprising administering to asubject in need thereof a therapeutically effective amount of aHDL-raising or HDL mimicking agent, in particular a CETPinhibitor/modulator, wherein the subjects treated have an improvedresponse genotype at rs11647778 and optionally rs1967309.

In another embodiment, the invention provides a method for treating orpreventing a cardiovascular disorder, comprising administering to asubject in need thereof an amount of an HDL-raising or HDL mimickingagent, in particular a CETP inhibitor/modulator, that is effective fortreating or preventing the cardiovascular disorder, wherein the subjecthas an improved response genotype at rs11647778 and optionallyrs1967309.

In another embodiment, the invention provides a method for treating orpreventing a cardiovascular disorder, comprising administering to asubject having an improved response genotype at rs11647778 andoptionally rs1967309, a therapeutically effective amount of aHDL-raising or HDL mimicking agent, in particular a CETPinhibitor/modulator.

In another embodiment, the invention provides a method for treating orpreventing a cardiovascular disorder, comprising administering to asubject having an improved response genotype at rs11647778 andoptionally rs1967309, an amount of an HDL-raising or HDL mimickingagent, in particular a CETP inhibitor/modulator that is effective fortreating or preventing the cardiovascular disorder.

In a particular embodiment, the invention provides the HDL-raising orHDL mimicking agent, in particular a CETP inhibitor/modulator for use inthe treatment or prevention of cardiovascular disorder, wherein thesubject treated carries an improved response genotype rs11647778.

In a particular embodiment, the invention provides the HDL-raising orHDL mimicking agent as herein defined wherein the improved responsegenotype is CC.

In a particular embodiment, the invention provides the HDL-raising orHDL mimicking agent, in particular a CETP inhibitor/modulator, for usein the treatment or prevention of a cardiovascular disorder in asubject, wherein the subject carries an improved response genotypers11647778. In a particular embodiment, the invention provides theHDL-raising or HDL mimicking agent as herein defined, wherein theimproved response genotype at rs11647778 is CC.

In a particular embodiment, the invention provides an HDL-raising or HDLmimicking agent as herein described, wherein the cardiovascular disorderis selected from the group consisting of atherosclerosis, peripheralvascular disease, dyslipidemia, hyperbetalipoproteinemia,hypoalphalipoproteinemia, hypercholesterolemia, hypertriglyceridemia,familial-hypercholesterolemia, angina, ischemia, cardiac ischemia,stroke, myocardial infarction, reperfusion injury, angioplasticrestenosis, hypertension, and vascular complications of diabetes,obesity or endotoxemia in a mammal.

In a particular embodiment, the invention provides the HDL-raising orHDL mimicking agent as herein described, wherein the cardiovasculardisorder is cardiovascular disease, coronary heart disease, coronaryartery disease, hypoalphalipoproteinemia, hyperbetalipoproteinemia,hypercholesterolemia, hyperlipidemia, atherosclerosis, hypertension,hypertriglyceridemia, hyperlipidoproteinemia, peripheral vasculardisease, angina, ischemia or myocardial infarction.

In a particular embodiment, the invention provides the HDL-raising orHDL mimicking agent as herein described, wherein the HDL-raising ormimicking agent is a HDL-raising agent, particularly a CETPinhibitor/modulator, more particularly isS-(2-{[1-(2-ethyl-butyl)-cyclohexanecarbonyl]-amino}-phenyl) ester.

In another embodiment, the invention providesS-(2-{[1-(2-ethyl-butyl)-cyclohexanecarbonyl]-amino}-phenyl) ester fortreating or preventing a cardiovascular disorder in a subject in needthereof, who has the genotype rs11647778/CC and optionallyrs12595857/GG, rs1967309/AA, rs111590482/AG, rs111590482/GG,rs11647828/GG, rs12935810/GG, rs17136707/GG, rs2239310/GG, rs2283497/AA,rs2531967/AA, rs3730119/AA, rs4786454/AA, rs74702385/GA, rs74702385/AA,rs8049452/GG, rs2238448/TT, or rs8061182/AA, more particularly whereinthe genotype is rs11647778/CC and optionally rs1967309/AA.

In another embodiment, the invention providesS-(2-{[1-(2-ethyl-butyl)-cyclohexanecarbonyl]-amino}-phenyl) ester fortreating or preventing patient with cardiovascular disorder, who carriesan improved response genotype, in particular wherein the genotype isrs11647778/CC and optionally rs12595857/GG, rs1967309/AA,rs111590482/AG, rs111590482/GG, rs11647828/GG, rs12935810/GG,rs17136707/GG, rs2239310/GG, rs2283497/AA, rs2531967/AA, rs3730119/AA,rs4786454/AA, rs74702385/GA, rs74702385/AA, rs8049452/GG orrs8061182/AA, more particularly wherein the genotype is rs11647778/CCand optionally rs1967309/AA.

In a particular embodiment, the invention providesS-(2-{[1-(2-ethyl-butyl)-cyclohexanecarbonyl]-amino}-phenyl) ester fortreating or preventing a patient with a cardiovascular disorder whocarries an improved response genotype, wherein the cardiovasculardisorder is selected from the group consisting of atherosclerosis,peripheral vascular disease, dyslipidemia, hyperbetalipoproteinemia,hypoalphalipoproteinemia, hypercholesterolemia, hypertriglyceridemia,familial-hypercholesterolemia, angina, ischemia, cardiac ischemia,stroke, myocardial infarction, reperfusion injury, angioplasticrestenosis, hypertension, and vascular complications of diabetes,obesity or endotoxemia in a mammal.

In a particular embodiment, the invention providesS-(2-{[1-(2-ethyl-butyl)-cyclohexanecarbonyl]-amino}-phenyl) ester fortreating or preventing a cardiovascular disorder in a subject in needthereof who has an improved response genotype, wherein thecardiovascular disorder is atherosclerosis, peripheral vascular disease,dyslipidemia, hyperbetalipoproteinemia, hypoalphalipoproteinemia,hypercholesterolemia, hypertriglyceridemia,familial-hypercholesterolemia, angina, ischemia, cardiac ischemia,stroke, myocardial infarction, reperfusion injury, angioplasticrestenosis, hypertension, and a vascular complication of diabetes,obesity or endotoxemia.

In a particular embodiment, the invention providesS-(2-{[1-(2-ethyl-butyl)-cyclohexanecarbonyl]-amino}-phenyl) ester fortreating or preventing a patient with a cardiovascular disorder whocarries an improved response genotype, wherein the cardiovasculardisorder is selected from the group consisting of cardiovasculardisease, coronary heart disease, coronary artery disease,hypoalphalipoproteinemia, hyperbetalipoproteinemia,hypercholesterolemia, hyperlipidemia, atherosclerosis, hypertension,hypertriglyceridemia, hyperlipidoproteinemia, peripheral vasculardisease, angina, ischemia, and myocardial infarction.

In a particular embodiment, the invention providesS-(2-{[1-(2-ethyl-butyl)-cyclohexanecarbonyl]-amino}-phenyl) ester fortreating or preventing a cardiovascular disorder in a subject in needthereof who has an improved response genotype, wherein thecardiovascular disorder is cardiovascular disease, coronary heartdisease, coronary artery disease, hypoalphalipoproteinemia,hyperbetalipoproteinemia, hypercholesterolemia, hyperlipidemia,atherosclerosis, hypertension, hypertriglyceridemia,hyperlipidoproteinemia, peripheral vascular disease, angina, ischemia,or myocardial infarction.

In another embodiment, the invention provides a method of predictingwhether a patient diagnosed with or having one or more symptoms of acardiovascular disease has an increased likelihood of benefiting fromtreatment with an HDL-raising or HDL mimicking agent, in particular aCETP inhibitor/modulator, comprising screening a sample obtained fromsaid patient for a genetic marker in the Adenylate Cyclase Type 9 gene(ADCY9) selected from rs11647778/CC, rs12595857/GG, rs1967309/AA,rs111590482/AG, rs111590482/GG, rs11647828/GG, rs12935810/GG,rs17136707/GG, rs2239310/GG, rs2283497/AA, rs2531967/AA, rs3730119/AA,rs4786454/AA, rs74702385/GA, rs74702385/AA, rs8049452/GG, rs2238448/TT,or rs8061182/AA, wherein the presence of the genetic marker indicatesthat the patient has an increased likelihood of benefiting from saidtreatment with an HDL-raising or HDL mimicking agent. In a particularembodiment, the genetic marker screened is rs11647778/CC and optionallyrs12595857/GG, rs2238448/TT, and/or rs1967309/AA. More particularly thegenetic marker screened is rs11647778/CC and optionally rs1967309/AA.

In another embodiment, the invention provides a method of predictingwhether a cardiovascular disorder patient has an increased likelihood ofbenefiting from treatment with a HDL-raising or HDL mimicking agent, inparticular a CETP inhibitor/modulator, comprising screening a sampleisolated from said patient for a genetic marker in the Adenylate CyclaseType 9 gene (ADCY9) selected from rs11647778/CC, rs12595857/GG,rs1967309/AA, rs111590482/AG, rs111590482/GG, rs11647828/GG,rs12935810/GG, rs17136707/GG, rs2239310/GG, rs2283497/AA, rs2531967/AA,rs3730119/AA, rs4786454/AA, rs74702385/GA, rs74702385/AA, rs8049452/GG,rs8061182/AA, wherein the patient has an increased likelihood ofbenefiting from said treatment with an HDL-raising or HDL mimickingagent. In a particular embodiment, the genetic marker screened isrs11647778/CC and optionally selected from rs12595857/GG; rs1967309/AA.More particularly the genetic marker screened is rs11647778/CC andoptionally rs1967309/AA.

In a further embodiment, the invention provides a method of selecting apatient who is likely to respond to an HDL-raising or HDL mimickingagent, the method comprising:

-   -   (a) determining the genotype at rs11647778 in a sample from a        patient diagnosed with or having one or more symptoms of a        cardiovascular disorder, and    -   (b) selecting a patient with genotype CC as more likely to        respond to an HDL-raising or HDL mimicking agent.

In yet a further embodiment, the method further comprises determiningthe genotype at rs1967309 and/or rs2238448, and selecting a patient withgenotype AA at rs1967309 and/or genotype TT at rs2238448 as likely torespond to an HDL-raising or HDL mimicking agent. In certainembodiments, the method further comprises administering an HDL-raisingor HDL mimicking agent (e.g. dalcetrapib) to the selected patient.

In a further embodiment, the invention provides a method of selecting apatient with a cardiovascular disorder as likely to respond to a therapycomprising HDL-raising or HDL mimicking agent, the method comprising:

-   -   (a) detecting an CC genotype at rs11647778 in a sample from the        patient,    -   (b) selecting the patient as more likely to respond to a therapy        comprising HDL-raising or HDL mimicking agent when rs11647778        with CC genotype is detected in the sample from the patient.

In yet a further embodiment, the invention provides a method ofselecting a patient with a cardiovascular disorder as likely to respondto a therapy comprising HDL-raising or HDL mimicking agent, the methodcomprising:

-   -   (a) detecting an CC genotype at rs11647778 and AA genotype at        rs1967309 in a sample from the patient,    -   (b) selecting the patient as more likely to respond to a therapy        comprising HDL-raising or HDL mimicking agent when rs11647778        with CC and rs1967309 with AA genotype is detected in the sample        from the patient.

In a particular embodiment, the invention provides the method hereindescribed, wherein the presence of an CC genotype at rs11647778 in areference sample (prior to the therapy with a HDL-raising or HDLmimicking agent according to the invention) indicates that the patientis more likely to respond to the therapy with a HDL-raising or HDLmimicking agent.

In a particular embodiment, the invention provides the method hereindescribed, wherein the presence of CC genotype at rs11647778 and AAgenotype at rs1967309 in a reference sample indicates that the patientis more likely to respond to the therapy with a HDL-raising or HDLmimicking agent.

In a particular embodiment, the invention provides the method hereindescribed which further comprises c) selecting the therapy comprising aHDL-raising or HDL mimicking agent.

In a particular embodiment, the invention provides the method hereindescribed wherein determining the genotype at rs11647778 in a samplefrom the patient comprises contacting the sample with agenotype-specific reagent (e.g. primer and/or probe) that binds to thers11647778 sequence, thereby forming a complex between the reagent andrs11647778 sequence, and detecting the complex formed, therebydetermining the genotype at rs11647778.

A method for determining the prognosis of a clinical response in a humanpatient to a HDL-raising or HDL mimicking agent, comprising determiningthe presence of at least one polymorphism in the ADCY9 gene of thepatient in which the polymorphism site is associated with a delayed,partial sub-optimal or lacking clinical response to said HDL-raising ormimicking agent wherein at least one polymorphism site is rs11647778.

A method for determining the prognosis of a clinical response in a humanpatient to a HDL-raising or HDL mimicking agent, comprising determiningthe presence of at least one polymorphism in the ADCY9 gene of thepatient in which the polymorphism site is associated with a delayed,partial sub-optimal or lacking clinical response to said HDL-raising ormimicking agent wherein at least two polymorphism sites are rs11647778and rs1967309.

In another embodiment, the invention provides a method for determiningthe prognosis of a clinical response in a human patient to a HDL-raisingor HDL mimicking agent, comprising determining the genotype of at leastone polymorphism site in the ADCY9 gene of the patient in which thepolymorphism site is associated with a delayed, partial sub-optimal orlacking clinical response to said HDL-raising or mimicking agent. In oneembodiment, the polymorphism site is rs11647778 and the GG genotype isindicative of a delayed, partial sub-optimal or lacking clinicalresponse to said HDL-raising or mimicking agent. In another embodiment,the polymorphism site is rs1967309 and the GG genotype is indicative ofa delayed, partial sub-optimal or lacking clinical response to saidHDL-raising or mimicking agent. In another embodiment, the polymorphismsite is rs2238448 and the CC genotype is indicative of a delayed,partial sub-optimal or lacking clinical response to said HDL-raising ormimicking agent.

In a particular embodiment, the invention provides the method hereindescribed, wherein the polymorphism is determined by a genotypinganalysis.

In a particular embodiment, the invention provides the method hereindescribed, wherein the genotyping analysis comprises a microarrayanalysis or a mass-spectrometric analysis or the use ofpolymorphism-specific primers and/or probes, in particular a primerextension reaction.

In a particular embodiment, the invention provides the method hereindescribed, wherein HDL-raising or HDL mimicking agent is a HDL-raisingagent, in particular a CETP inhibitor/modulator, more particularlyS-(2-{[1-(2-ethyl-butyl)-cyclohexanecarbonyl]-amino}-phenyl) ester.

In a particular embodiment, the “CETP inhibitor/modulator” isthioisobutyric acidS-(2-{[1-(2-ethyl-butyl)-cyclohexanecarbonyl]-amino}-phenyl) ester, alsoknown asS-[2-([[1-(2-ethylbutyl)-cyclohexyl]-carbonyl]amino)phenyl]2-methylpropanethioate,dalcetrapib or a compound of formula I

S-[2-([[1-(2-ethylbutyl)cyclohexyl] carbonyl] amino) phenyl]2-methylpropanethioate has been shown to be an inhibitor of CETPactivity in humans (de Grooth et al., Circulation, 105, 2159-2165(2002)) and rabbits (Shinkai et al., J. Med. Chem., 43, 3566-3572(2000); Kobayashi et al., Atherosclerosis, 162, 131-135 (2002); andOkamoto et al., Nature, 406 (13), 203-207 (2000)).S-[2-([[1-(2-ethylbutyl) cyclohexyl] carbonyl] amino) phenyl]2-methylpropanethioate has been shown to increase plasma HDL cholesterolin humans (de Grooth et al., supra) and in rabbits (Shinkai et al.,supra; Kobayashi et al., supra; Okamoto et al., supra). Moreover,S-[2-([[1-(2-ethylbutyl) cyclohexyl] carbonyl] amino) phenyl]2-methylpropanethioate has been shown to decrease LDL cholesterol inhumans (de Grooth et al., supra) and rabbits (Okamoto et al., supra).S-[2-([[1-(2-ethylbutyl)cyclohexyl] carbonyl] amino) phenyl]2-methylpropanethioate, as well as methods of making and using thecompound, are described in EP1020439, Shinkai et al., J. Med. Chem.43:3566-3572 (2000) or WO 2007/051714, WO 2008/074677 or WO2011/000793.

In a preferred embodiment the CETP inhibitor/modulator (e.g. compound offormula I) is a solid in crystalline or amorphous form, or morepreferably in crystalline form. In a particular embodimentS-[2-([[1-(2-ethylbutyl)-cyclohexyl]-carbonyl]amino)phenyl]2-methylpropanethioateis in crystalline form A as disclosed in WO2012/069087. Form A ischaracterized by an X-ray powder diffraction pattern having peaks atabout 7.9°, 8.5°, 11.7°, 12.7°, 17.1°, 18.0°, 18.5°, 20.2°, 22.1°,24.7°±0.2°, particularly by an XRPD peaks observed at an angle ofdiffraction 2Theta of 7.9°, 11.7°, 17.1°, 18.5° (±0.2°).

Other CETP inhibitors known in the art and useful in the presentinvention include: evacetrapib, anacetrapib and torcetrapib,particularly evacetrapib and anacetrapib.

Accordingly, the invention provides a method for the treatment orprevention of a cardiovascular disorder in a mammal, which methodcomprises administering to a mammal (preferably a mammal in needthereof) a therapeutically effective amount of the pharmaceuticalcomposition. The mammal preferably is a human (i.e., a male or femalehuman). The human can be of any race (e. g., Caucasian or Oriental).

The cardiovascular disorder particularly is atherosclerosis, peripheralvascular disease, dyslipidemia, hyperbetalipoproteinemia,hypoalphalipoproteinemia, hypercholesterolemia, hypertriglyceridemia,familial-hypercholesterolemia, angina, ischemia, cardiac ischemia,stroke, myocardial infarction, reperfusion injury, angioplasticrestenosis, hypertension, and vascular complications of diabetes,obesity or endotoxemia. More particularly, the cardiovascular disorderis cardiovascular disease, coronary heart disease, coronary arterydisease, hypoalphalipoproteinemia, hyperbetalipoproteinemia,hypercholesterolemia, hyperlipidemia, atherosclerosis, hypertension,hypertriglyceridemia, hyperlipidoproteinemia, peripheral vasculardisease, angina, ischemia or myocardial infarction.

In certain embodiments of the present invention, the subjects orpatients are administered between 100 mg to 600 mg ofS-[2-([[1-(2-ethylbutyl)-cyclohexyl]-carbonyl]amino)phenyl]2-methylpropanethioate.In particular, the subjects or patients are administered between 150 mgto 450 mg ofS-[2-([[1-(2-ethylbutyl)-cyclohexyl]-carbonyl]amino)phenyl]2-methylpropanethioate.More particularly, the subjects or patients are administered between 250mg to 350 mg ofS-[2-([[1-(2-ethylbutyl)-cyclohexyl]-carbonyl]amino)phenyl]2-methylpropanethioate.Most particularly, the subjects or patients are administered between 250mg to 350 mg ofS-[2-([[1-(2-ethylbutyl)-cyclohexyl]-carbonyl]amino)phenyl]2-methylpropanethioate.

In another embodiment of the present invention, the subject forpediatric use are administered between 25 mg to 300 mg ofS-[2-([[1-(2-ethylbutyl)-cyclohexyl]-carbonyl]amino)phenyl]2-methylpropanethioate.In particular the subject for pediatric use are administered 75 mg to150 mg ofS-[2-([[1-(2-ethylbutyl)-cyclohexyl]-carbonyl]amino)phenyl]2-methylpropanethioate.

The CETP inhibitor can be administered to the mammal at any suitabledosage (e. g., to achieve a therapeutically effective amount). Forexample, a suitable dose of a therapeutically effective amount ofS-[2-([[1-(2-ethylbutyl)-cyclohexyl]-carbonyl]amino)phenyl]2-methylpropanethioatefor administration to a patient will be between approximately 100 mg toabout 1800 mg per day. A desirable dose is preferably about 300 mg toabout 900 mg per day. A preferred dose is about 600 mg per day.

Genotyping Methods

Identification of the particular genotype of a DNA sample may beperformed by any of a number of methods well known to one of skill inthe art. For example, identification of the polymorphism can beaccomplished by cloning of the allele and sequencing it using techniqueswell known in the art. Alternatively, the gene sequences can beamplified from genomic DNA, e.g. using PCR, and the product sequenced.Numerous methods are known in the art for isolating and analyzing asubject's DNA for a given genetic marker including polymerase chainreaction (PCR), ligation chain reaction (LCR) or ligation amplificationand amplification methods such as self sustained sequence replication.Several non-limiting methods for analyzing a patient's DNA for mutationsat a given genetic locus are described below.

DNA microarray technology, e.g., DNA chip devices and high-densitymicroarrays for high-throughput screening applications and lower-densitymicroarrays, may be used. Methods for microarray fabrication are knownin the art and include various inkjet and microjet deposition orspotting technologies and processes, in situ or on-chipphotolithographic oligonucleotide synthesis processes, and electronicDNA probe addressing processes. The DNA microarray hybridizationapplications has been successfully applied in the areas of geneexpression analysis and genotyping for point mutations, singlenucleotide polymorphisms (SNPs), and short tandem repeats (STRs).Additional methods include interference RNA microarrays and combinationsof microarrays and other methods such as laser capture micro-dissection(LCM), comparative genomic hybridization (CGH) and chromatinimmunoprecipitation (ChiP). See, e.g., He et al. (2007) Adv. Exp. Med.Biol. 593: 117-133 and Heller (2002) Annu. Rev. Biomed. Eng. 4: 129-153.Other methods include PCR, xMAP, invader assay, mass spectrometry, andpyrosequencing (Wang et al. (2007) Microarray Technology and Cancer GeneProfiling Vol 593 of book series Advances in Experimental Medicine andBiology, pub. Springer New York).

Another detection method is allele specific hybridization using probesoverlapping the polymorphic site and having about 5, or alternatively10, or alternatively 20, or alternatively 25, or alternatively 30nucleotides around the polymorphic region. For example, several probescapable of hybridizing specifically to the allelic variant or geneticmarker of interest are attached to a solid phase support, e.g., a“chip”. Oligonucleotide probes can be bound to a solid support by avariety of processes, including lithography. Mutation detection analysisusing these chips comprising oligonucleotides, also termed “DNA probearrays” is described e.g., in Cronin et al. (1996) Human Mutation7':244.

In other detection methods, it is necessary to first amplify at least aportion of the gene prior to identifying the allelic variant.Amplification can be performed, e.g., by PCR and/or LCR or other methodswell known in the art.

In some cases, the presence of the specific allele in DNA from a subjectcan be shown by restriction enzyme analysis. For example, the specificnucleotide polymorphism can result in a nucleotide sequence comprising arestriction site which is absent from the nucleotide sequence of anotherallelic variant.

In a further embodiment, protection from cleavage agents (such as anuclease, hydroxylamine or osmium tetroxide and with piperidine) can beused to detect mismatched bases in RNA/RNA DNA/DNA, or RNA/DNAheteroduplexes (see, e.g., Myers et al. (1985) Science 230: 1242). Ingeneral, the technique of “mismatch cleavage” starts by providingduplexes formed by hybridizing a probe, e.g., RNA or DNA, which isoptionally labeled, comprising a nucleotide sequence of the allelicvariant of the gene with a sample nucleic acid, obtained from a tissuesample. The double-stranded duplexes are treated with an agent thatcleaves single-stranded regions of the duplex such as those formed frombase pair mismatches between the control and sample strands. Forinstance, RNA/DNA duplexes can be treated with RNase and DNA/DNA hybridstreated with SI nuclease to enzymatically digest the mismatched regions.Alternatively, either DNA/DNA or RNA/DNA duplexes can be treated withhydroxylamine or osmium tetroxide and with piperidine in order to digestmismatched regions. After digestion of the mismatched regions, theresulting material is then separated by size on denaturingpolyacrylamide gels to determine whether the control and sample nucleicacids have an identical nucleotide sequence or in which nucleotides theyare different. See, for example, U.S. Pat. No. 6,455,249; Cotton et al.(1988) Proc. Natl. Acad. Sci. USA 85:4397; Saleeba et al. (1992) Meth.Enzymol. 217:286-295.

Alterations in electrophoretic mobility may also be used to identify theparticular allelic variant. For example, single strand conformationpolymorphism (SSCP) may be used to detect differences in electrophoreticmobility between mutant and wild type nucleic acids (Orita et al. (1989)Proc Natl. Acad. Sci USA 86:2766; Cotton (1993) Mutat. Res. 285: 125-144and Hayashi (1992) Genet. Anal. Tech. Appl. 9:73-79). Single-strandedDNA fragments of sample and control nucleic acids are denatured andallowed to renature. The secondary structure of single-stranded nucleicacids varies according to sequence; the resulting alteration inelectrophoretic mobility enables the detection of even a single basechange. The DNA fragments may be labeled or detected with labeledprobes. The sensitivity of the assay may be enhanced by using RNA(rather than DNA), in which the secondary structure is more sensitive toa change in sequence. In another preferred embodiment, the subjectmethod utilizes heteroduplex analysis to separate double strandedheteroduplex molecules on the basis of changes in electrophoreticmobility (Keen et al. (1991) Trends Genet. 7:5).

The identity of the allelic variant or genetic marker may also beobtained by analyzing the movement of a nucleic acid comprising thepolymorphic region in polyacrylamide gels containing a gradient ofdenaturant, which is assayed using denaturing gradient gelelectrophoresis (DGGE) (Myers et al. (1985) Nature 313:495). When DGGEis used as the method of analysis, DNA will be modified to ensure thatit does not completely denature, for example by adding a GC clamp ofapproximately 40 bp of high-melting GC-rich DNA by PCR. In a furtherembodiment, a temperature gradient is used in place of a denaturingagent gradient to identify differences in the mobility of control andsample DNA (Rosenbaum and Reissner (1987) Biophys. Chem. 265: 1275).

Examples of techniques for detecting differences of at least onenucleotide between 2 nucleic acids include, but are not limited to,selective oligonucleotide hybridization, selective amplification, orselective primer extension. For example, oligonucleotide probes may beprepared in which the known polymorphic nucleotide is placed centrally(allele-specific probes) and then hybridized to target DNA underconditions which permit hybridization only if a perfect match is found(Saiki et al. (1986) Nature 324: 163); Saiki et al. (1989) Proc. Natl.Acad. Sci. USA 86:6230). Such allele specific oligonucleotidehybridization techniques are used for the detection of the nucleotidechanges in the polymorphic region of the gene. For example,oligonucleotide probes having the nucleotide sequence of the specificallelic variant are attached to a hybridizing membrane and this membraneis then hybridized with labeled sample nucleic acid. Analysis of thehybridization signal will then reveal the identity of the nucleotides ofthe sample nucleic acid.

Alternatively, allele specific amplification technology which depends onselective PCR amplification may be used in conjunction with the instantinvention. Oligonucleotides used as primers for specific amplificationmay carry the allelic variant of interest in the center of the molecule(so that amplification depends on differential hybridization) (Gibbs etal. (1989) Nucl. Acids Res. 17:2437-2448) or at the extreme 3′ end ofone primer where, under appropriate conditions, mismatch can prevent, orreduce polymerase extension (Prossner (1993) Tibtech 11:238 and Newtonet al. (1989) Nucl. Acids Res. 17:2503). This technique is also termed“PROBE” for PRobeOligo Base Extension. In addition it may be desirableto introduce a novel restriction site in the region of the mutation tocreate cleavage-based detection (Gasparini et al. (1992) Mol. Cell.Probes 6: 1).

In another embodiment, identification of the allelic variant or geneticmarker is carried out using an oligonucleotide ligation assay (OLA), asdescribed, e.g., in U.S. Pat. No. 4,998,617 and in Laridegren, U. et al.Science 241: 1077-1080 (1988). The OLA protocol uses two oligonucleotideprobes which are designed to be capable of hybridizing to abuttingsequences of a single strand of a target. One of the oligonucleotides islinked to a separation marker, e.g., biotinylated, and the other isdetectably labeled. If the precise complementary sequence is found in atarget molecule, the oligonucleotides will hybridize such that theirtermini abut, and create a ligation substrate. Ligation then permits thelabeled oligonucleotide to be recovered using avidin, or another biotinligand. Nickerson, D. A. et al. have described a nucleic acid detectionassay that combines attributes of PCR and OLA (Nickerson, D. A. et al.(1990) Proc. Natl. Acad. Sci. USA 87:8923-8927). In this method, PCR isused to achieve the exponential amplification of target DNA, which isthen detected using OLA. A variation of the OLA method as described inTobe et al. (1996) Nucleic Acids Res. 24: 3728 each allele specificprimers is labeled with a unique hapten, i.e. digoxigein and floresceinand each OLA reaction is detected using hapten specific antibodieslabeled with reporter enzymes.

The invention provides methods for detecting a single nucleotidepolymorphism (SNP) in ADCY9. Because single nucleotide polymorphisms areflanked by regions of invariant sequence, their analysis requires nomore than the determination of the identity of the single variantnucleotide and it is unnecessary to determine a complete gene sequencefor each patient. Several methods have been developed to facilitate theanalysis of SNPs.

The single base polymorphism can be detected by using a specializedexonuclease-resistant nucleotide, as disclosed, e.g., in U.S. Pat. No.4,656,127. According to the method, a primer complementary to theallelic sequence immediately 3′ to the polymorphic site is permitted tohybridize to a target molecule obtained from a particular animal orhuman. If the polymorphic site on the target molecule contains anucleotide that is complementary to the particular exonuclease-resistantnucleotide derivative present, then that derivative will be incorporatedonto the end of the hybridized primer. Such incorporation renders theprimer resistant to exonuclease, and thereby permits its detection.Since the identity of the exonuclease-resistant derivative of the sampleis known, a finding that the primer has become resistant to exonucleasesreveals that the nucleotide present in the polymorphic site of thetarget molecule was complementary to that of the nucleotide derivativeused in the reaction. This method has the advantage that it does notrequire the determination of large amounts of extraneous sequence data.

A solution-based method may also be used to determine the identity ofthe nucleotide of the polymorphic site (WO 91/02087). As above, a primeris employed that is complementary to allelic sequences immediately 3′ toa polymorphic site. The method determines the identity of the nucleotideof that site using labeled dideoxynucleotide derivatives, which, ifcomplementary to the nucleotide of the polymorphic site will becomeincorporated onto the terminus of the primer.

An alternative method is described in WO 92/15712. This method usesmixtures of labeled terminators and a primer that is complementary tothe sequence 3′ to a polymorphic site. The labeled terminator that isincorporated is thus determined by, and complementary to, the nucleotidepresent in the polymorphic site of the target molecule being evaluated.The method is usually a heterogeneous phase assay, in which the primeror the target molecule is immobilized to a solid phase.

Many other primer-guided nucleotide incorporation procedures forassaying polymorphic sites in DNA have been described (Komher, J. S. etal. (1989) Nucl. Acids. Res. 17:7779-7784; Sokolov, B. P. (1990) Nucl.Acids Res. 18:3671; Syvanen, A.-C, et al. (1990) Genomics 8:684-692;Kuppuswamy, M. N. et al. (1991) Proc. Natl. Acad. Sci. USA 88:1143-1147; Prezant, T. R. et al. (1992) Hum. Mutat. 1: 159-164;Ugozzoli, L. et al. (1992) GATA 9: 107-112; Nyren, P. et al. (1993)Anal. Biochem. 208: 171-175). These methods all rely on theincorporation of labeled deoxynucleotides to discriminate between basesat a polymorphic site.

Moreover, it will be understood that any of the above methods fordetecting alterations in a gene or gene product or polymorphic variantscan be used to monitor the course of treatment or therapy.

The methods described herein may be performed, for example, by utilizingpre-packaged diagnostic kits, such as those described below, comprisingat least one probe, primer nucleic acid, or reagent which may beconveniently used for genotyping, e.g., analyzing a genetic markerpresent in the ADCY9 gene to determine whether an individual has anincreased likelihood of benefiting from treatment with HDL-raising ormimicking agent including a HDL-raising or HDL mimicking agent, inparticular a CETP inhibitor/modulator. In particular the genetic markersare as described herein.

Primers or probes of the present invention, for use as reagents forgenotyping genetic markers present in the ADCY9 gene, comprise asynthetic nucleotide sequence that is complimentary to and hybridizeswith a contiguous sequence within the ADCY9 gene, of preferably 12 to 30nucleotides, adjacent to or encompassing one or more SNPs selected fromrs11647778, rs1967309, rs12595857, rs2239310, rs11647828, rs8049452,rs12935810, rs74702385, rs17136707, rs8061182, rs111590482, rs4786454,rs2283497, rs2531967, rs3730119, rs2238448 and rs13337675, preferablyrs11647778. In other aspects a primer comprises 100 or fewernucleotides, in certain aspects from 12 to 50 nucleotides or from 12 to30 nucleotides. The primer is at least 70% identical to the contiguoussequence or to the complement of the contiguous nucleotide sequence,preferably at least 80% identical, and more preferably at least 90%identical. A primer or probe of the invention is preferably 15-50nucleotides in length comprising a region of 15 to 20 nucleotides thatis complimentary to a sequence selected from SEQ. ID. NO 1-21, inparticular is complementary to sequence SEQ. ID No 1, 19 or 21. Thedegree of complimentary between a probe or primer and SEQ. ID. NO. 1-21maybe 100%, 95%, 90%, 85%, 80% or 75%.

Oligonucleotides, including probes and primers, “specific for” a geneticallele or genetic marker bind either to the polymorphic region of a geneor bind adjacent to the polymorphic region of the gene. Foroligonucleotides that are to be used as primers for amplification,primers are adjacent if they are sufficiently close to be used toproduce a polynucleotide comprising the polymorphic region. In oneembodiment, oligonucleotides are adjacent if they bind within about 1-2kb, e.g. less than 1 kb from the polymorphism. Specific oligonucleotidesare capable of hybridizing to a sequence, and under suitable conditionswill not bind to a sequence differing by a single nucleotide.

Oligonucleotides of the invention, whether used as probes or primers,can be detectably labeled. Labels can be detected either directly, forexample for fluorescent labels, or indirectly. Indirect detection caninclude any detection method known to one of skill in the art, includingbiotin-avidin interactions, antibody binding and the like. Fluorescentlylabeled oligonucleotides also can contain a quenching molecule.Oligonucleotides can be bound to a surface. In some embodiments, thesurface is silica or glass. In some embodiments, the surface is a metalelectrode.

Probes can be used to directly determine the genotype of the sample orcan be used simultaneously with or subsequent to amplification. The term“probes” includes naturally occurring or recombinant single- ordouble-stranded nucleic acids or chemically synthesized nucleic acids.They may be labeled by nick translation, Klenow fill-in reaction, PCR orother methods known in the art. Probes of the present invention, theirpreparation and/or labeling are described in Sambrook et al. (1989)supra. A probe can be a polynucleotide of any length suitable forselective hybridization to a nucleic acid containing a polymorphicregion of the invention. Length of the probe used will depend, in part,on the nature of the assay used and the hybridization conditionsemployed.

Labeled probes also can be used in conjunction with amplification of apolymorphism. (Holland et al. (1991) Proc. Natl. Acad. Sci. USA88:7276-7280). U.S. Pat. No. 5,210,015 describes fluorescence-basedapproaches to provide real time measurements of amplification productsduring PCR. Such approaches have either employed intercalating dyes(such as ethidium bromide) to indicate the amount of double-stranded DNApresent, or they have employed probes containing fluorescence-quencherpairs (also referred to as the “TaqMan®” approach) where the probe iscleaved during amplification to release a fluorescent molecule whoseconcentration is proportional to the amount of double-stranded DNApresent. During amplification, the probe is digested by the nucleaseactivity of a polymerase when hybridized to the target sequence to causethe fluorescent molecule to be separated from the quencher molecule,thereby causing fluorescence from the reporter molecule to appear. TheTaqMan® approach uses a probe containing a reporter molecule-quenchermolecule pair that specifically anneals to a region of a targetpolynucleotide containing the polymorphism.

Probes can be affixed to surfaces for use as “gene chips.” Such genechips can be used to detect genetic variations by a number of techniquesknown to one of skill in the art. In one technique, oligonucleotides arearrayed on a gene chip for determining the DNA sequence of a by thesequencing by hybridization approach, such as that outlined in U.S. Pat.Nos. 6,025,136 and 6,018,041. The probes of the invention also can beused for fluorescent detection of a genetic sequence. Such techniqueshave been described, for example, in U.S. Pat. Nos. The probes of theinvention also can be used for fluorescent detection of a geneticsequence. Such techniques have been described, for example, in U.S. Pat.Nos. 5,968,740 and 5,858,659. A probe also can be affixed to anelectrode surface for the electrochemical detection of nucleic acidsequences such as described in U.S. Pat. No. 5,952,172 and by Kelley, S.O. et al. (1999) Nucl. Acids Res. 27:4830-4837. One or more probes fordetecting the SNP of the invention (Table 2, 3, 4, 5 or 10, inparticular Table 4) can be affixed to a chip and such a device used topredict response to HDL-raising or HDL mimicking agent, in particularCETP inhibitor/modulator and select an effective treatment for anindividual with cardiovascular disease. It is conceivable that probesfor detecting the SNP of the invention could be included on a chip witha variety of other probes for uses other than predicting response to aHDL-raising or HDL mimicking agent, in particular CETPinhibitor/modulator.

Additionally, synthetic oligonucleotides used as probes or primers maybe modified to become more stable. Exemplary nucleic acid moleculeswhich are modified include uncharged linkages such as phosphoramidate,phosphothioate and methylphosphonate analogs of DNA (see also U.S. Pat.Nos. 5,176,996; 5,264,564 and 5,256,775). Primers and probes of theinvention can include for example, labeling methylation,inter-nucleotide modification such as pendent moieties (e.g.,polypeitides), intercalators (e.g., acridine, psoralen), chelators,alkylators, and modified linkages (e.g., alpha anomeric nucleic acids).Also included are synthetic molecules that mimic nucleotide acidmolecules in the ability to bind to a designated sequence by hydrogenbonding and other chemical interactions, including peptide linkages thatsubstitute for phosphate linkages in the nucleotide backbone.

The invention relates to synthetic oligonucleotide molecules, primersand probes that hybridize under high stringency hybridization conditionsto naturally occurring oligonucleotides described herein, gene markersof the ADCY9 gene. Oligonucleotides can be detected and/or isolated byspecific hybridization, under high stringency conditions. “Highstringency conditions” are known in the art and permit specifichybridization of a first oligonucleotide to a second oligonucleotidewhere there is a high degree of complimentarity between the first andsecond oligonucleotide. For the genotyping methods disclosed herein thisdegree of complimentarity is between 80% and 100% and preferably between90% and 100%

The SNPs of the invention can also be detected from pre-existing data,such as whole genome sequence data present in a data base. The inventionprovides a computer implemented method of querying genomic data todetermine a genotype for predicting the response of a patient to a CETPinhibitor and treating said patient accordingly i.e. treating responderpatients with a CETP inhibitor.

Sample nucleic acid for use in the genotyping methods, treatmentselection or methods of treatment can be obtained from any cell type ortissue of a subject. For example, a subject's bodily fluid, a sample,(e.g. blood) can be obtained by known techniques. Alternatively, nucleicacid tests can be performed on dry samples (e.g., hair or skin). Moreparticularly, the sample nucleic acid for genotyping methods, treatmentselection or methods of treatment will be obtained from blood cell type.

The invention described herein relates to methods and reagents usefulfor determining and identifying the allele present on the ADCY9 gene atrs11647778 and optionally rs1967309, rs2238448 or rs12595857, or anyother genetic variant in linkage disequilibrium with these SNPs such asdisplayed in FIGS. 8 and 9, spanning from position chr16:4049365 tochr16:4077178 (assembly GRCh37/hg19). In particular the invention alsorelates to methods and reagents for determining and identifying theallele present in the ADCY9 gene at rs11647778 and optionally rs1967309,rs12595857, rs2239310, rs11647828, rs8049452, rs12935810, rs74702385,rs17136707, rs8061182, rs111590482, rs4786454, rs2283497, rs2531967,rs3730119, rs13337675, rs2238448 more particularly at rs11647778 andoptionally rs1967309 and/or rs12595857, and most particularly atrs11647778 and optionally rs1967309.

As set forth herein, the invention also provides treatment selectionmethods comprising detecting one or more genetic markers present in theADCY9 gene. In some embodiments, the methods use probes or primerscomprising nucleotide sequences which are complementary to a polymorphicregion of ADCY9. Accordingly, the invention provides kits comprisingprobes and primers for performing the genotyping methods of theinvention.

In some embodiments, the invention provides kits useful for determiningwhether a patient with a cardiovascular disorder has an increasedlikelihood of benefiting from treatment with a HDL-raising or HDLmimicking agent, in particular a CETP inhibitor/modulator. Such kitscontain one of more of the reagents, in particular primers or probes,described herein and instructions for use. As an example only, theinvention also provides kits useful for determining whether a patientwith cardiovascular disorder has an increased likelihood of benefitingfrom treatment with thioisobutyric acidS-(2-{[1-(2-ethyl-butyl)-cyclohexanecarbonyl]-amino}-phenyl) estercomprising a first oligonucleotide and a second oligonucleotidesspecific for a CC polymorphism in the ADCY9 rs11647778 SNP andoptionally for a AA polymorphism in the ADCY9 rs1967309 SNP.

The kits can comprise at least one probe or primer that is capable ofspecifically hybridizing to the polymorphic region of ADCY9 andinstructions for use. The kits can comprise at least one of the abovedescribed nucleic acids. Kits useful for amplifying at least a portionof ADCY9 generally comprise two primers, at least one of which iscapable of hybridizing to the allelic variant sequence. Such kits aresuitable for detection of genotype by, for example, fluorescencedetection, by electrochemical detection, or by other detection.

Yet other kits of the invention comprise at least one reagent useful toperform the assay. For example, the kit can comprise an enzyme.Alternatively the kit can comprise a buffer or any other useful reagent.

The kits can include all or some of the positive controls, negativecontrols, reagents, primers, sequencing markers, probes and antibodiesdescribed herein for determining the subject's genotype in thepolymorphic region of ADCY9.

The following examples are intended merely to illustrate the practice ofthe present invention and are not provided by way of limitation.

The present invention refers to the following nucleotide and amino acidsequences:

The sequences provided herein are available in the NCBI database and canbe retrieved from www.ncbi.nlm.nih.gov/sites/entrez?db=gene; Thesessequences also relate to annotated and modified sequences. The presentinvention also provides techniques and methods wherein homologoussequences, and variants of the concise sequences provided herein areused. Preferably, such “variants” are genetic variants. ON NCB1 databasethe Nucleotide sequence encoding Homo sapiens Adenylate Cyclase Type 9(ACDY9) is available.

Homo sapiens Adenylate Cyclase Type 9 (ADCY9), RefSeqGene on chromosome16 NCBI Reference Sequence: NCBI accession number NG_011434.1

Homo sapiens chromosome 16 genomic contig, GRCh37.p10 Primary AssemblyNCBI Reference Sequence: NCBI accession number NT_010393.16

The intronic sequences for Homo sapiens ACDY9 gene SNPs providing the“rs” designation, alleles and corresponding SEQ ID number designationsis disclosed in Tables 6, 7 and 8. The polymorphisms are identified inbold and within bracket.

TABLE 6 ACDY9 SNPs and respective intronic sequence SEQ. SNP rs IDID. NO.: Intronic sequence¹ HGVS Names rs11647778 21 GGACCTGCCTGGTGNC_000016.10:g.4001379C > G CTTTCTCAGAG[C/G] NG_011434.1:g.119807G > CAGACTGAGGTTTGG NM_001116.3:c.1884 + 5989G > C GGTTTGCGGAANT_010393.17:g.3991379C > G rs1967309 20 TTAACCTATTTATTTNC_000016.9:g.4065583A > G CTTTCAACCCT[C/T] NG_011434.1:g.105604T > CAGCCCAGATCCTAA NM_001116.3:c.1694 - 8024 > C CCTTCGGTAAGNT_010393.16:g.4005583A > G   rs12595857 2 CATTGATTTTAAACNC_000016.9:g.4062592G > A CTCAACAACAGC[A/G] NG_011434.1:g.108595C > TATGTCTTTTATCA NM_001116.3:c.1694-5033C > T GCTTAATTTTACNT_010393.16:g.4002592G > A ¹Source from NCBI Genome reference Build37.3

TABLE 7List of genetic variants in gene ADCY9 on chr16 which have provided evidence ofassociation (P < 0.05) with response to treatment with dalcetrapib from theGWAS study with reference sequence from the genotyping chip used for theexperiment (Illumina OMNI2.5S): Position SNPrs (GRCh37/ identifier Chr.hg19) (NCBI) P value Sequence^(1,2) SEQ. ID NO. 16 4,065,583 rs19673094.11E-08 TTCATGCACCCA  1 GCAGACTAAATG TTTACTGAGTAC TTACCGAAGGTTAGGATCTGGGCT [A/G]AGGGTTGA AAGAAATAAATA GGTTAAAAAAGA AAAAAAGCCACCTAGGTGACTTTC ACTC¹ 16 4,062,592 rs12595857 4.53E-07 TTAATATGATTT  2CTTATATTCTTTC CTGGTTATCCAT TGATTTTAAACC TCAACAACAGC [A/G]ATGTCTTTTATCAGCTTAATT TTACAAAGGCTA CAGAGAGGGGT GGGCATTTCCTA ATGG² 16 4,060,661rs2239310 1.29E-06 CCTGTGTGGAGC  3 CCATTACCTGAA GAGGGGCCAAG AGGACAAGCAGGTATGACTATGG TC[A/G]GGCGTG CCAAGTCCCAGG ACAAGGAAGGA CGGGTGCTCCAGGAAGCACAGGA GGGGGCAT² 16 4,051,513 rs11647828 2.76E-06 TACCGGATGGCA  4GTGAGCAGGGA GGCTCACCTGGA TCATTTGGTGAA GGTGGCATCTGC C[T/C]GGTTTGTCCACTGTGAAGTT CCTATTCCTACC CCGCCCCCCACC TTTCTTTTTTGAG ATG² 16 4,076,094rs8049452 6.63E-06 ACTTAACTATTT  5 GTTGGGTGAATA TAGAAATGAATGAATGAATGGATG GATGAGCAGATA [T/C]ATCAAGAA GTTAATTCACAA ATTAAAGCCCATTATGAAACTAAA GTAGAGGCTGGG CGCG¹ 16 4,049,365 rs12935810 2.98E-05ACCCGTGAACAA  6 GTCGGGCCCCCA TCCACGCAATAT CTGCAGTCTCGA CTGTATGATCTC[A/G]TCCTTTGCA GCCACACTGTGA GGCAGCAATGAT CATTCCGCAGAC GGCCACAGACTC CAG²16 4,065,495 rs74702385 8.87E-05 GACGACACCCAG  7 CACACCCAGCACACCCAGCACACC AGCGAACAGCCC ACCAGGTGCTAT [T/C]GCTGTCATT CATTTGCTCATTCGCTCGTTCATG CACCCAGCAGAC TAAATGTTTACT GAG¹ 16 4,076,047 rs171367079.11E-05 AAAACAGTGCTC  8 CAAAGGCAAAG AAATAGCAAAG ACAGAAGTAAGGCACTTAACTAT TTG[T/C]TGGGTG AATATAGAAATG AATGAATGAATG GATGGATGAGCAGATACATCAAGA AGTTAA¹ 16 4,070,333 rs8061182 1.51E-04 GGCAGCTATGTA  9GGAAGCAGTGA AGATCCACATCC TTCCTTATTGGT GAAAGGAATGA AT[T/C]GGAAACAGAAAGTTCTTT TTTACCTTTATTA AATAAACGTGAA GTCATAAGAACT ACTAA² 16 4,064,368rs111590482 1.64E-04 AGACTTTGTCTC 10 AAAAAAGAAAA AAAAAAAAAAAGAAGTCCCAAAT AATAAAATATGA GA[T/C]GGATTT ATGGAAGAAAGT GAAAGAAACAAAGGGTAGGCACC TTGCCTGTTTAA TTTGATC¹ 16 4,076,136 rs4786454 1.98E-04TGGATGGATGAG 11 CAGATACATCAA GAAGTTAATTCA CAAATTAAAGCC CATTATGAAACT[A/G]AAGTAGAG GCTGGGCGCGGT GGATCACGCCTA TAATCCCAGCAC TTTGGGAGGTCA AGGC²16 4,066,061 rs2283497 8.87E-04 TGTGATATGATG 12 GTCATATCATAGCACAGGGCTGTT GTGAGGATTAAA TGAGTTGATTCA [T/G]GTAAACAGG GACATCCGAAAAAGGGAAAGACG GTGCTTGTCCTG AGAACAGCTGTG AATG¹ 16 4,052,486 rs25319671.11E-03 AGGTGAGTGGCC 13 TTAAAGGGGAAG GAGAAACCTTTT GAAAGCAGGACAGGTCCTCTCTG A[A/G]TCATCCCC GTATGGGTAAAT CTACATCACTAG CTTCATTACTGACTGGTCCATGTA GAAA¹ 16 4,057,603 rs3730119 0.0108 CAGGTATGTCTT 14CAAACCTATGAT GGATAAAAGTTA CAGTCAGCACAG ATTGAAAGCACC [A/G]TCTGTTGAAACGCAGCTCCGT CTTGCTCTCTGG AGAGGACTCACT CCTGGAAAGTTG AGA² 16 4,077,178rs13337675 0.0377 TGTAACCAAGTA 15 ACCAATGGTAAA CCTCTACAGGGT ATTAAGGCTCCAGAAAATTCTCTA [A/G]TCAGCCACT TGCTCCTGCTCG AGCCTGCTCCCA CTCCGTGGAGTGTACTTTCATTTCA GT¹ Chr: chromosome number; P value: for association withcardiovascular events (primary composite event or unanticipated coronaryrevascularization) in patients treated with the CETP inhibitordalcetrapib; 1: Reference sequence from the 1000 Genomes publicdatabase, as presented in the ILLUMINA annotation file for the OMNI 2.5SChip HumanOmni25Exome-8v1_A.csv; 2: Reference sequence from the dbSNPpublic database version 131 from NCBI, as presented in the ILLUMINAannotation file for the OMNI 2.5S Chip HumanOmni25Exome-8v_1A. csv.

TABLE 8 List of additional genetic variants in gene ADCY9 on chr16:Distance SEQ. (bp) ID Variation Location¹ from a r2¹ D′¹ Column²HGV Names² NO. rs12920508 16:4066891  1308 0.952954 1 TTTGGGGTGACGNC_000016.9:g.4066891 16 AAAATGTAAAAT G > C TA[C/G/T]GTTGTNC_000016.9:g.4066891 GGTGATGGTTGC G > T ACAACACC NG_011434.1:g.104296C > A NG_011434.1:g.104296 C > G NM_001116.3:c.1694 - 9332C > ANM_001116.3:c.1694 - 9332C > G NT_010393.16:g.400689 1G > CNT_010393.16:g.400689 1G > T rs12599911 16:4062436  3147 0.908417 1GAATAACCACAC NC_000016.9:g.4062436 17 ACATGGACCCTG G > T GG[G/T]TCCAAGNG_011434.1:g.108751 TTCATTAGAATG C > A GCTCTTT NM_001116.3:c.1694 -4877C > A NT_010393.16:g.400243 6G > T rs2531971 16:4051261 143220.840627 0.973493 AAGACAGAGGA NC_000016.9:g.4051261 18 ACCCCCATAGGCC > A TGG[G/T]GGTGA NG_011434.1:g.119926 GCAGGGGGCATG G > T AGGGCTAANM_001116.3:c.1884 + 6108G > T NT_010393.16:g.399126 1C > A rs223844816:4059439  6144 0.840582 0.973467 TGTCCAACTATT NC_000016.9:g.4059439 19TCTTTCTTTCTTT T > C T[C/T]TGAGATGG NG_011434.1:g.111748 GGGTCTCACTGTA > G GTTGG NM_001116.3:c.1694 - 1880A > G NT_010393.16:g.399943 9T > CReferences: a. rs1967309 ¹Location r2 and D′ values from the 1000Genomes public database ²Reference sequence &HGV Names from the dbSNPpublic database version 137 from NCBI

Example 1

Dal-OUTCOMES trial (NC20971) was a double blind, randomized,placebo-controlled, parallel group, multi-center, phase III study toassess the safety and efficacy of the CETP inhibitor dalcetrapib inpatients recently hospitalized for an Acute Coronary Syndrome (ACS). Attime of the interim analysis the study included 15871 randomizedpatients, distributed over two treatment arms: placebo (7933 patients)and dalcetrapib (600 mg daily; 7938 patients). The study has shown noevidence of reduction of the event rate in the primary efficacy endpointin the dalcetrapib arm compared to the placebo arm. The dal-OUTCOMESstudy details can be found in G. Schwartz et al., N. Engl. J. Med. 367;22, 2012.

dal-Outcomes patients were recruited 4 to 12 weeks followinghospitalization for acute coronary syndrome characterized by elevatedcardiac biomarkers, with symptoms of acute myocardial ischemia, ischemicelectrocardiographic abnormalities that were new or presumed to be new,or loss of viable myocardium on imaging. Patients without elevatedcardiac biomarkers were eligible to participate if symptoms of acutemyocardial ischemia were accompanied by electrocardiographic changesthat were new or presumed to be new and by additional evidence ofobstructive coronary disease. (Schwartz G G et al. Am Heart J 2009;158:896-901 e3). Patients who had a myocardial infarction associatedwith percutaneous coronary intervention were also eligible. All patientswere following individualized programs to target LDL cholesterol levelsof 100 mg per deciliter (2.6 mmol per liter) or lower by statin iftolerated and diet. No specific statin agent was specified, and patientswere not excluded based on LDL cholesterol values. Patients with serumtriglyceride levels of 400 mg per deciliter (4.5 mmol per liter) orhigher were excluded. (Schwartz G G et al. N Engl J Med 2012;367:2089-99) Eligible participants to the dal-Outcomes trial entered asingle-blind placebo run-in period of approximately 4 to 6 weeks toallow for patients to stabilise and for completion of plannedrevascularisation procedures. At the end of the run-in period, eligiblepatients in stable condition were randomised in a 1:1 ratio to 600 mg ofdalcetrapib or placebo on top of evidence-based medical care for acutecoronary syndrome. Cardiovascular events were adjudicated by anindependent clinical endpoint committee. For the pharmacogenomics study,6338 patients were recruited from April 2008 through July 2010 at 461sites in 14 countries and provided written informed consent toparticipate to the genetic study of the dal-OUTCOMES trial. DNA wasextracted from whole blood. Following genomic data cleanup, samples from5749 Caucasian patients were used for the discovery genome-wideassociation study (GWAS).

Genotyping

The Illumina Infinium HumanOmni2.5Exome-8v1_A BeadChip including2,567,845 genetic variants (Illumina, San Diego, Calif.) was used forthe discovery GWAS of 5749 Caucasian participants to the dal-OUTCOMESstudy. The chromosome 16 region including 5 genes upstream anddownstream of the adenylate cyclase type 9 (ADCY9) gene (CHR16:3,400,000-4,600,000) was imputed using IMPUTE2, providing 17,764variants for analysis with an average completion rate of 99.76%. ASequenom panel was used for the confirmation of imputed singlenucleotide polymorphisms (SNPs) in the ADCY9 gene identified indal-OUTCOMES and were tested in the dal-PLAQUE-2 study, including 20SNPs with P values <0.05 from the discovery GWAS.

DNA was extracted from 1 ml of whole blood using the QiaSymphony DNAmidi kit version 1.1 (Qiagen, Garstilgweg, Switzerland) and quantifiedusing the QuantiFluor™ dsDNA System (Promega, Madison, Wis.) with anaverage concentration of 91.5 ng/μL and average yield of 18.3 μg. 97.9%of DNA samples had concentrations above 25 ng/μL. Agarose gelelectrophoresis confirmed high quality of DNA with no signs ofdegradation. DNA was normalized to 50 ng/μL.

Genome-Wide Association Study (GWAS)—

Genome-wide genotyping was performed using 200 ng of genomic DNA inGLP-environment at the Beaulieu-Saucier Pharmacogenomics Centre(Montreal, Canada). The Illumina Infinium HumanOmni2.5Exome-8v1_ABeadChip (Illumina, San Diego, Calif.) including 2,567,845 genomicmarkers was used and processed according to the manufacturer'sspecifications. This chip includes over 200,000 exome variantsidentified through the Exome Chip Consortium. The remaining BeadChipcontent is a mix of rare and common SNPs from the 1000 Genome Projectdesigned to be maximally informative for diverse world populations. EachBeadChip was scanned and analyzed using the Illumina iScan Reader.Scanned images were analyzed using Illumina's GenomeStudio version2011.1 with the GenTrain 2.0 cluster algorithm, using a No-Callthreshold of 0.15, without manual cluster adjustment and using themanufacturer's Illumina HumanOmni25Exome-8v1_A cluster file. Genotypedata files were produced in three installments of comparable size asdata became available.

Sequenom—

A single Sequenom panel was designed and validated using HapMap DNAsamples. The panel included 27 SNPs in the ADCY9 gene selected accordingto: a P value ≤0.05 in the discovery GWAS (n=15), a P value <10⁻⁶ byimputation (n=6; 1 failed in development), predicted regulatory function(n=5; 1 excluded due to low MAF), or literature (n=4; 1 failed inproduction). The Sequenom MassArray Maldi-TOF System (Sequenom, LaJolla, Calif.) was used with Sequenom's Typer 4.0.22 Software. Eachplate was clustered using autocluster and manually modified as needed.Two Coriell Institute DNA samples (NA11993 and NA07357) used as controlson each genotyping plate showed 100% concordance on all plate replicatesand 100% concordance of genotype calls with expectations forcorresponding SNPs in the 1000 Genomes and HapMap reference database. 17SNPs genotyped on both the GWAS and Sequenom panel provided a meangenotypic concordance of 99.95% (min: 99.41, max: 100.00%), and 11 SNPspreviously imputed provided a mean genotypic concordance with the mostlikely genotype (>0.80 imputation probability) of 99.75 (min: 98.48,max: 99.96).

Genomic Quality Checks

Dal-Outcomes Discovery GWAS.

Three genotyping files in PLINK format generated by GenomeStudio werecombined and transformed to binary PLINK format. GenomeStudio Finalreport files were used to generate gender plots, LRR and BAF graphics.PyGenClean (Lemieux Perreault L P et al. Bioinformatics 2013; 29:1704-5)and PLINK version 1.07 were used for the quality checks (QC) and geneticdata cleanup process. The genotyping experiment consisted of 68 platesof DNA samples. On each plate, there were two controls, one Coriell DNAalternating from four pre-selected samples (NA11993, NA11992, NA10860and NA12763) and one internal DNA control from four pre-selectedsamples. The pairwise concordance of Coriell samples ranged from0.999807 to 0.999958. Pairwise concordance of the four internal controlsranged from 0.99976 to 0.99995. The comparison of Coriell genotypes toexpectation from the 1000 Genomes data provided concordance ranging from0.996028 to 0.997783.

Detailed genetic data cleanup steps are presented in Table 9. DuplicatedSNPs were evaluated for concordance, completion rate, allele call andMAF. SNPs with different allele calls or different MAF were retained.Identical and concordant SNPs were merged. Genotyping completion ratefor samples and SNPs was set to 98%. SNPs with genotyping plate bias(based on the 96 well plates used to dilute DNA samples) were flaggedbut not removed as the effect of genetic ancestry could not be excluded.Pairwise identity-by-state (IBD) was used to conduct close familialrelationship checks. All but one pair-member of related pairs and sampleduplicates (IBS2*ratio>0.80) were flagged and removed based on aselection of uncorrelated SNPs (r²<0.1). The pairwise IBS matrix wasused as a distance metric to identify cryptic relatedness among samplesand sample outliers by multi-dimensional scaling (MDS). The first twoMDS components of each subject were plotted including the genotypes ofHapMap CEU, JPT-CHB, and YRI data (keeping only founder individuals).Outliers from the main Caucasian cluster were flagged and removed byk-nearest neighbour (FIG. 5). The scree plot and the cumulativeexplained variance were computed using the smartpca program of theEIGENSOFT suite (version 3.0). Options used were a numoutlieriter(maximum number of outlier removal iterations) of 0 (turned off) andaltnormstyle (normalization formula) equal to NO. (Price A L Nat Genet2006; 38:904-9) (FIG. 6)

Imputation

The chromosome 16 region including 5 genes upstream and downstream ofADCY9 (CHR16: 3,401,847-4,598,558; NCBI build GRCh37) was imputed usingthe programs IMPUTE2 (version 2.3.0) and GTOOL (version 0.7.0) on Linuxwith 1096 genotyped SNPs and 5749 dal-Outcomes Caucasian samples. (HowieB N et Al. PLoS Genet 2009; 5:e1000529) Strand alignment was solved byautomatically flipping non A/T and C/G SNPs according to position.Ambiguous A/T and C/G SNPs were considered missing and were imputed. TheImpute2 reference package ALL_1000G_phase1integrated_v3_chr16_impute wasused for imputation. We used a cut-off of 0.80 for imputed genotypeprobabilities per genotype and per individual and a completion rate of98% or higher. There remained 17,764 variants for analysis with anaverage completion rate of 99.76%.

Of 1,223,798 common SNPs analyzed, a single region with genome-widesignificance was found to be associated with cardiovascular events byCox proportional hazards modeling in the dalcetrapib arm, identifying aSNPs in the ADCY9 gene on chromosome 16: rs1967309 (P=2.41×10⁻⁸) (FIG.1A). The genetic variant at this position has a minor allele frequencyof 0.41, and the additive genetic effect of one allele (A) has a HR=0.65(95% CI 0.56, 0.76) for cardiovascular events in the dalcetrapib arm(Table 12a). Neighbouring SNPs in linkage disequilibrium with rs1967309and which provided lower, but supporting evidence for association werelocated in a common recombination block (FIG. 1B). Imputation in thisregion identified 9 additional SNPs in the ADCY9 gene with P<10⁻⁵,including 6 with P<10⁻⁶ (FIG. 10). None of the 835,255 rare SNPsanalyzed in 36,268 SKAT gene sets passed the significance threshold forfollow-up.

There was no detectable genetic effect for rs1967309 in the placebo armalone (Cox proportional-hazards, HR=0.92; P=0.25) (Table 12b). Thegene-by-treatment arm interaction term was indicative of a statisticalinteraction (P=0.0014; beta: −0.340). Stratification by genotypes in thedalcetrapib arm shows that homozygotes for the minor allele (AA) andheterozygotes (AG) at rs1967309 have respectively HR=0.40 (95% CI 0.28,0.57) and HR=0.68 (95% CI 0.55, 0.84) for cardiovascular events whencompared to reference GG homozygotes (FIG. 3). Considering only patientswith the homozygous genotype AA at rs1967309 (n=961), there was a 39%reduction in the pre-specified composite endpoint of coronary heartdisease death, resuscitated cardiac arrest, non-fatal myocardialinfarction, non-fatal ischemic stroke, unstable angina or unanticipatedcoronary revascularization with dalcetrapib compared to placebo(HR=0.61; 95% CI 0.41, 0.92). Similar results were observed whencoronary revascularizations were removed from the primary endpoint(HR=0.60; 95% CI 0.35, 1.02). When considering only patients with thehomozygous genotype GG at rs1967309 (n=1984), there was a 27% increasein cardiovascular events for treatment with dalcetrapib versus placebo(HR=1.27; 95% CI 1.02, 1.58). Heterozygous carriers had an intermediateresponse (n=2796; HR=0.94; 95% CI 0.77, 1.16). Results were confirmed bygenotyping 27 SNPs in the ADCY9 gene by Sequenom technology (Table 10).

A total of eight polymorphisms (genotyped or imputed) were associatedwith P values less than 10⁻⁶ in the discovery cohort of 5749 patientsfrom the pharmacogenomic study of the dal OUTCOMES trial, with theprespecified primary composite endpoint of coronary heart disease death,resuscitated cardiac arrest, non-fatal myocardial infarction, non-fatalischemic stroke, unstable angina with objective evidence of ischemia orcoronary revascularization. In this discovery genome-wide analysis, twoof these eight SNPs in the ADCY9 gene were associated with P-values lessthan 5×10⁻⁸. For the polymorphic nucleotide rs1967309, patients with theAA genotype (minor, or less common, allele) benefited from a reductionin cardiovascular events of 39% when treated with dalcetrapib comparedto placebo, whereas those with the GG genotype (major allele) wereexposed to a 27% increase in risk. Heterozygous patients with the AGgenotype had an intermediate response. These results were only observedwith dalcetrapib, not in the placebo arm, and there were statisticalinteractions between the polymorphisms and the study arm (dalcetrapibversus placebo) in the association with clinical events thusstrengthening the link with the ADCY9 gene. Hazard ratios were similarwhen coronary revascularizations were removed from the analysis, whichprovided a direct comparison with the primary composite endpoint of theglobal dal-OUTCOMES trial (coronary heart disease, resuscitated cardiacarrest, non-fatal myocardial infarction, non-fatal ischemic stroke orunstable angina). All eight polymorphisms were in strong linkagedisequilibrium (r²>0.77), which reinforces the postulate that thisregion of the ADCY9 gene determines clinical responses to dalcetrapib.

Plasma LIPIDS

Genotypes of rs1967309 SNPs were significantly associated with changesover time in lipids induced by dalcetrapib in dal-OUTCOMES. Usingunivariate statistics, genotypes were associated with change in totalcholesterol at 1 month (P=0.0001; P=0.004 when controlling for genderand genetic ancestry): GG genotype carriers had a smaller increase(10.0±23.3 mg/dl) compared to AG (12.9±30.3) and AA (13.8±24.0)carriers. This effect was not observed in the placebo arm. A similarresult was observed for change in LDL-cholesterol after 1 month ofdalcetrapib treatment: Changes were −2.0±20.0, −1.0±20.0 and +0.6±21.0mg/dl in GG, AG and AA genotype carriers of rs1967309 respectively(P=0.003 univariate; adjusted P=0.006). During the dalcetrapib treatmentperiod, GG carriers had overall slightly lower LDL-cholesterol levels(adjusted P=0.048; repeated measures analysis, FIG. 4).

TABLE 9 Summary information of the genetic data clean-up proceduresperformed prior to statistical analysis Procedure Clean-up step N SNPIDs Number of SNPs in genotyping file 2,567,845 Number of samples ingenotyping file 6,528 SNPs without physical position removed 6,913−6,913 Insertion/deletion variants removed 169 −169 Genotyping controlsNA10860 17 NA11992 17 −67 NA11993 17 NA12763 16 Internal qualitycontrols 68 −68 Samples destroyed due to duplicate ids 68 −68 Samplesfailed in lab 25 −25 Duplicate SNPs (by physical position) 42,360Triplicate SNPs (by physical position) 460 Quadruplicate SNPs (byphysical position) 2 Replicated SNPs merged (same alleles) 42,722−42,722 Replicated SNPs not merged 458 Replicated SNPs with <98%concordance 46 −46 Samples with >10% missing genotypes 3 −3 SNPswith >2% missing genotypes 46,542 −46,542 Samples with >2% missinggenotypes 0 SNPs with plate-bias P < 1 · 10⁻⁷ 275 flagged SNPs used forIBS analysis 77,689 SNPs used for MDS analysis 76,854 No sex (missingfrom clinical file) 64 Gender problem 301 Related pairs 16 Ethnicityother than Caucasian by MDS 436 −548² cluster Internal QC controls 12Haploid genotypes (after gender 3,063,235 Set to issues processed)missing SNPs with MAF = 0 408,652 −408,652 HWE test 2.46 · 10⁻⁸ < P <10⁻⁴ 3,993 flagged HWE test P < 2.46 · 10⁻⁸ (0.05/2,062,801) 3748 −3,748Total number of SNPs for analysis 2,059,053 Total number of samples foranalysis 5,749 ¹One sample was identified as possible XO/XX mosaic andwas removed from the analysis set. ²There were 10 samples having morethan one reason for exclusion from the data set.

TABLE 10 Hazard Ratio (HR) fortime to events (first occurrence of CHDdeath, MI, hospitalization for ACS, resuscitated cardiac arrest,atherothrombotic stroke or unanticipated coronary revascularization) onthe dalcetrapib treatment arm versus the placebo arm stratified bygenotypes of SNPs identified to be associated with cardiovascular eventsin the ADCY9 gene. Treatment effects of dalcetrapib versus placebostratified by genotype for 20 validation SNPs genotyped in 5686 patientsof the dal-Outcomes study population genotyped by Sequenom. MAF (minorallele frequency) and r2 were evaluated on all available individuals (n= 5686) NR = non-responsive; PR = partially responsive; R = responsive:N N patients patients Responsive- SNP rs r² with Hazard ratio withwithout P ness to minor major identifier MAF rs1967309 Genotype N (dalvs placebo) events events value treatment allele allele rs1967309 0.41071 GG 1970 1.248 (1.002, 1.556) 320 1650 0.048 NR A G AG 2761 0.953(0.776, 1.172) 362 2399 0.6498 PR AA 955 0.625 (0.415, 0.941) 96 8590.0242 R rs2531971 0.4341 0.849171 CC 1805 1.254 (0.997, 1.577) 294 15110.0536 NR A C AC 2812 0.965 (0.787, 1.181) 374 2438 0.727 PR AA 10570.660 (0.449, 0.968) 108 949 0.0336 R rs2238448 0.4585 0.81182 CC 16591.291 (1.016, 1.641) 271 1388 0.0364 NR T C CT 2830 0.974 (0.796, 1.192)377 2453 0.7984 PR TT 1188 0.657 (0.462, 0.934) 128 1060 0.0192 Rrs11647778 0.4586 0.778951 GG 1658 1.300 (1.023, 1.651) 271 1387 0.0318NR C G CG 2841 0.966 (0.79, 1.182) 378 2463 0.7371 PR CC 1187 0.691(0.488, 0.98) 129 1058 0.038 R rs12599911 0.4442 0.869138 TT 1742 1.244(0.984, 1.574) 281 1461 0.068 NR G T GT 2832 0.982 (0.804, 1.200) 3842448 0.8609 PR GG 1108 0.672 (0.462, 0.98) 112 996 0.0388 R rs125958570.4467 0.861475 AA 1730 1.255 (0.992, 1.586) 281 1449 0.0584 NR G A AG2828 0.954 (0.780, 1.167) 379 2449 0.6469 PR GG 1124 0.719 (0.499,1.038) 117 1007 0.078 R rs12920508 0.4123 0.985041 CC 1891 1.205 (0.964,1.506) 310 1581 0.1016 NR G C CG 2672 0.946 (0.766, 1.169) 345 23270.6072 PR GG 928 0.676 (0.451, 1.014) 96 832 0.0585 R rs11647828 0.43780.696167 TT 1786 1.315 (1.04, 1.663) 281 1505 0.0224 NR C T CT 28200.963 (0.788, 1.177) 381 2439 0.7121 PR CC 1079 0.647 (0.447, 0.936) 116963 0.0209 R rs2239310 0.3613 0.567866 AA 2303 1.150 (0.937, 1.413) 3651938 0.1814 NR G A AG 2657 0.971 (0.785, 1.201) 340 2317 0.7858 PR GG726 0.623 (0.388, 0.998) 73 653 0.049 R rs8049452 0.418 0.466547 CC 19090.804 (0.622, 1.041) 234 1675 0.0978 R T C CT 2798 0.971 (0.794, 1.187)380 2418 0.771 PR TT 977 1.543 (1.13, 2.106) 164 813 0.0064 NRrs12935810 0.4297 0.485354 GG 1830 0.796 (0.612, 1.036) 224 1606 0.0898R A G AG 2826 1.043 (0.853, 1.276) 379 2447 0.6802 NR AA 1030 1.260(0.935, 1.697) 175 855 0.1286 NR rs111590482 0.1254 0.210392 TT 43481.054 (0.902, 1.231) 637 3711 0.5095 NR C T CT 1250 0.856 (0.612, 1.198)137 1113 0.3643 R CC 88 0.333 (0.035, 3.205) 4 84 0.3414 R rs747023850.1251 0.210876 CC 4351 1.053 (0.902, 1.23) 639 3712 0.5147 NR T C CT1247 0.854 (0.609, 1.197) 135 1112 0.3593 R TT 88 0.348 (0.036, 3.348) 484 0.3608 R rs8061182 0.4052 0.467552 TT 1996 0.815 (0.636, 1.044) 2521744 0.1055 R C T CT 2772  0.99 (0.809, 1.212) 378 2394 0.9247 PR CC 918 1.52 (1.095, 2.11) 148 770 0.0124 NR rs17136707 0.1214 0.19852 TT 43561.058 (0.906, 1.235) 638 3718 0.4791 NR C T CT 1216 0.835 (0.592, 1.177)131 1085 0.3031 PR CC 78 0.552 (0.05, 6.096) 3 75 0.6281 R A G rs47864540.1675 0.280233 GG 3931 1.062 (0.903, 1.25) 582 3349 0.4677 NR AG 1579 0.91 (0.68, 1.217) 182 1397 0.5231 PR AA 160 0.573 (0.187, 1.751) 13147 0.3285 R rs2531967 0.2314 0.28616 GG 3374 1.121 (0.94, 1.337) 4962878 0.2046 NR A G AG 1992 0.855 (0.668, 1.094) 253 1739 0.2132 PR AA320 0.786 (0.379, 1.63) 29 291 0.5176 R rs2283497 0.3934 0.146627 GG2081 1.226 (0.977, 1.538) 301 1780 0.0781 NR T G GT 2735 0.999 (0.815,1.224) 372 2363 0.9926 PR TT 869 0.581 (0.39, 0.864) 105 764 0.0074 Rrs3730119 0.1766 0.16273 GG 3776 1.059 (0.894, 1.254) 539 3237 0.5058 NRA G AG 1657 0.887 (0.676, 1.165) 209 1448 0.3891 PR AA 159 0.472 (0.177,1.259) 18 141 0.1337 R rs13337675 0.247 0.141651 AA 3221 1.070 (0.891,1.284) 462 2759 0.4703 NR G A AG 2121 0.904 (0.715, 1.143) 280 18410.3996 PR GG 344 1.034 (0.537, 1.989) 36 308 0.9206 PR

TABLE 11 r2 value between all SNPs based on 5686 from the dal-Outcomesstudy. rs- rs- rs- rs- 12935810 2531971 11647778 11647828 rs2531967rs3730119 rs2238448 rs2239310 rs12599911 rs12595857 rs12935810 0.53900.4591 0.4143 0.1347 0.1255 0.4525 0.3865 0.5501 0.5586 rs2531971 0.90260.8171 0.2639 0.2567 0.8608 0.6398 0.9073 0.9211 rs11647778 0.91210.3619 0.2324 0.9549 0.5764 0.8302 0.8410 rs11647828 0.3900 0.15210.8722 0.4991 0.7502 0.7616 rs2531967 0.0607 0.3462 0.0384 0.2456 0.2523rs3730119 0.2316 0.3572 0.2461 0.2453 rs2238448 0.6011 0.8658 0.8589rs2239310 0.6925 0.6903 rs12599911 0.9850 rs12595857 rs111590482rs74702385 rs1967309 rs2283497 rs12920508 rs8061182 rs17136707 rs8049452rs4786454 rs13337675 rs- rs- rs- rs- 111590482 74702385 1967309 2283497rs12920508 rs8061182 rs17136707 rs8049452 rs4786454 rs13337675rs12935810 0.1083 0.1082 0.4854 0.3331 0.4907 0.7364 0.1022 0.73810.1415 0.1009 rs2531971 0.1666 0.1666 0.8492 0.1037 0.8567 0.4836 0.17700.4975 0.2434 0.2067 rs11647778 0.1514 0.1511 0.7790 0.1412 0.78420.5336 0.1633 0.5496 0.2280 0.1833 rs11647828 0.1651 0.1647 0.69620.1078 0.7006 0.4903 0.1762 0.5042 0.2487 0.1293 rs2531967 0.4159 0.41590.2862 0.0647 0.2906 0.1955 0.4198 0.2030 0.2530 0.0266 rs3730119 0.02550.0256 0.1627 0.1032 0.1626 0.1248 0.0215 0.1296 0.0366 0.1796 rs22384480.1734 0.1731 0.8118 0.1533 0.7994 0.5564 0.1670 0.5574 0.2309 0.1786rs2239310 0.2554 0.2541 0.5679 0.2531 0.5612 0.3668 0.2431 0.3772 0.33760.0497 rs12599911 0.1851 0.1843 0.8691 0.1282 0.8585 0.5321 0.17570.5325 0.2455 0.1951 rs12595857 0.1835 0.1827 0.8615 0.1254 0.86810.5212 0.1738 0.5353 0.2431 0.1968 rs111590482 0.9944 0.2104 0.22240.2030 0.1049 0.9276 0.1066 0.6329 0.0156 rs74702385 0.2109 0.22280.2033 0.1048 0.9283 0.1069 0.6337 0.0156 rs1967309 0.1466 0.9850 0.46760.1985 0.4665 0.2802 0.1417 rs2283497 0.1410 0.4353 0.2132 0.4492 0.08770.0011 rs12920508 0.4601 0.1917 0.4725 0.2740 0.1463 rs8061182 0.10220.8910 0.1342 0.0834 rs17136707 0.1086 0.6780 0.0151 rs8049452 0.14560.0959 rs4786454 0.0323 rs13337675

TABLE 12 Results with P < 5 × 10⁻⁸ in the dal-OUTCOMES discoverygenome-wide association study (GWAS) Patients Patients β_(g) P SNPGenotype group with events without events β_(g) ¹ value² HR (95% CI) a.Cox proportional-hazards results in the dal-OUTCOMES alcetrapib arm (n =2845) rs1967309 AA 38 447 −0.429 2.41 × 10⁻⁸ 0.651 (0.560, 0.757) AG 1761203 GG 176 802 b. Cox proportional-hazards results in the dal-OUTCOMESplacebo arm (n = 2904) rs1967309 AA 59 417 −0.085 0.248 0.916 (0.793,1.06)  AG 192 1225 GG 146 860 ¹Estimate of the regression parameter forthe additive genetic effect adjusted for gender and 5 principalcomponents for genetic ancestry, and where homozygotes for the commonallele are coded 0, heterozygotes 1, and homozygotes for the rare alleleare coded 2; ²Likelihood ratio test of the genotype effect, where H₀:β_(g) = 0; HR: hazard ratio; SNP: single nucleotide polymorphism.

Example 2

The dal-PLAQUE-2 study (Tardif J C et al, Circulation Cardiovascularimaging 2011; 4:319-33) was a phase 3b multicenter, double-blind,randomized, placebo-controlled, parallel group trial designed toevaluate the effect of dalcetrapib on atherosclerotic diseaseprogression in patients with evidence of coronary artery disease andcarotid intima media thickness of at least 0.65 mm in the far wall ofthe common carotid arteries, as assessed by B-mode ultrasonography. Atotal of 931 patients were randomized to receive dalcetrapib 600 mgdaily or matching placebo with intended treatment duration of 24 months.However, the trial was terminated prematurely concurrent with thetermination of dal OUTCOMES (the latter due to futility). Patientscontinued study medication until they returned for follow-up carotidimaging at 12 months. Carotid B-mode ultrasound recordings at baseline,month 6, and month 12 were analyzed centrally at the core laboratory ofthe Montreal Heart Institute. Intima-media thickness (IMT) was analyzedon the far wall of the common carotid arteries. A segment of 10 mm inlength of the common carotid artery was analyzed on serial examinationsusing an automated edge detection software (Carotid Analyzer, MedicalImaging Applications, Coralville, Iowa). Among the 411 participants inthe dal-PLAQUE-2 trial who consented to the genetic study, 386 hadimaging measures at baseline, 6 months and 12 months (194 and 192 in thedalcetrapib and placebo arms respectively). DNA was extracted from wholeblood. The research protocols were approved by the relevantinstitutional review boards or ethics committees and all humanparticipants gave written informed consent.

Central Analysis of Carotid Imaging Examinations in the Dal-Plaque-2Trial

All acquired carotid ultrasound recordings were analyzed at the corelaboratory of the Montreal Heart Institute by experienced technicianssupervised by a physician. Images were required to meet quality andinclusion and exclusion criteria for eligibility prior to randomassignment to study treatment. The methods for carotid intima-mediathickness analysis included side-by-side viewing of baseline andfollow-up studies.

Carotid arterial wall segments were assessed in a longitudinal view,perpendicular to the ultrasound beam, with a horizontal display of thearterial image in order to view the interfaces between blood andvascular structures on the longest possible segment. The localization ofthe end of the common carotid artery was used as the landmark inrepositioning and analyzing comparative length of segments in baselineand follow-up studies. Intima-media thickness was analyzed on the farwall of the right and left common carotid arteries, to reducevariability of measurements. The average of the mean intima-mediathickness values of the right and left common carotid arteries was used.A matched segment of 10 mm in length of the common carotid artery wasanalyzed on serial examinations (baseline, 6 months and 12 months),starting 5 mm proximal to the carotid bifurcation. The edge detectionsoftware Carotid Analyzer (Medical Imaging Applications LLC, Coralville,Iowa) was used to analyze intima-media thickness using the automatedoption. Two sets of carotid artery borders were identified: First, themedia-adventitia borders were determined and verified by the reader.When required, their locations were semi-automatically modified to thecorrect location. When these borders were approved, the lumen-intimaboundaries were automatically detected using the media-adventitiaborders for guidance. Frames from looped sequences of intima-mediathickness were selected for reading, and poor quality outlier frameswere removed from the analysis when required.

Of the 27 SNPs selected for genotyping by Sequenom, 20 SNPs in the ADCY9gene had P<0.05 in the discovery cohort. We tested for association withthose SNPs in the dal-PLAQUE-2 trial in order to obtain supportingevidence for association by relying on imaging data obtained after 6 and12 months of treatment in the dalcetrapib arm (n=194). Ten out of 20SNPs provided association with IMT measures in dal-PLAQUE-2 (P<0.05,Table 13). Notably, marker rs2238448 (which was in linkagedisequilibrium with rs1967309 (r²=0.80)) was associated with IMT indal-plaque-2 (P=0.009) and with events in dal-OUTCOMES (P=8.88×10⁻⁸;HR=0.67, 95% CI 0.58, 0.78). After 12 months of treatment withdalcetrapib, changes in IMT were −0.027±0.079 mm in homozygote carriersof the minor allele (TT), 0.000±0.048 mm for heterozygotes, and+0.009±0.038 mm for homozygous carriers of the common allele (CC) atrs2238448 (P=0.009). This effect emerged at 6 months. All 20 SNPsdisplayed a decrease in IMT in agreement with the genotype group thatshowed reduced cardiovascular risk in the dal-OUTCOMES trial (Table 13).None of the genotyped SNPs showed association in the placebo arm (allP>0.05). Only the gene-by-treatment interaction term of rs2531967reached significance (P=0.024) in dal-PLAQUE-2, probably due to thesmall sample size. SNP rs1967309 did not reach significance indal-PLAQUE-2 (P=0.114), but the reduction in IMT was of similarmagnitude to that with rs2238448 and consistent with the findings indal-OUTCOMES. After 12 months of treatment with dalcetrapib, changes inIMT were −0.021±0.083 mm in AA homozygotes, −0.001±0.048 mm forheterozygotes, and +0.005±0.042 mm for GG homozygotes at rs1967309.

TABLE 13 Change from baseline in carotid intima-media thickness after 6and 12 months of dalcetrapib treatment. 20 SNPs with P < 0.05 indal-OUTCOMES are shown with results for the dal-PLAQUE-2 study.dal-PLAQUE-2 Homozygotes for minor allele Heterozygotes Mean (±STD) Mean(±STD) SNP Position¹ MAF² visit N mm N mm rs1967309 16:4065583 0.411 M0630 −0.005 (±0.058) 99 −0.003 (±0.040) M12 26 −0.021 (±0.083) 90 −0.001(±0.048) rs2531971 16:4051261 0.434 M06 28 −0.010 (±0.065) 109 −0.002(±0.040) M12 25 −0.016 (±0.069) 99   0.002 (±0.045) rs2238448 16:40594390.459 M06 32 −0.010 (±0.061) 111 −0.003 (±0.040) M12 28 −0.027 (±0.079)102   0.000 (±0.048) rs11647778 16:4051380 0.459 M06 34 −0.013 (±0.062)109 −0.002 (±0.039) M12 30 −0.026 (±0.079) 99   0.001 (±0.047)rs12599911 16:4062436 0.444 M06 35 −0.008 (±0.068) 108 −0.003 (±0.036)M12 31 −0.019 (±0.086) 99 −0.002 (±0.044) rs12595857 16:4062592 0.447M06 36 −0.008 (±0.067) 107 −0.003 (±0.036) M12 32 −0.018 (±0.085) 98−0.002 (±0.044) rs12920508 16:4066891 0.42 M06 30 −0.005 (±0.058) 99−0.003 (±0.040) M12 26 −0.021 (±0.083) 90 −0.001 (±0.048) rs223931016:4060661 0.361 M06 22 −0.001 (±0.070) 98 −0.004 (±0.041) M12 19 −0.002(±0.074) 90 −0.003 (±0.050) rs11647828 16:4051513 0.438 M06 29 −0.018(±0.050) 106 −0.002 (±0.045) M12 25 −0.020 (±0.077) 97 −0.003 (±0.052)rs8049452 16:4076094 0.418 M06 31   0.020 (±0.049) 97 −0.002 (±0.035)M12 30   0.006 (±0.033) 90   0.003 (±0.046) rs12935810 16:4049365 0.43M06 30   0.021 (±0.050) 91 −0.003 (±0.035) M12 30   0.010 (±0.040) 83−0.001 (±0.043) rs8061182 16:4070333 0.405 M06 30   0.016 (±0.050) 94  0.000 (±0.035) M12 29 −0.001 (±0.045) 87   0.007 (±0.042) rs7470238516:4065495 0.125 M06 3 −0.015 (±0.035) 46 −0.006 (±0.039) M12 3 −0.008(±0.058) 37 −0.002 (±0.047) rs17136707 16:4076047 0.121 M06 3 −0.015(±0.035) 46 −0.006 (±0.038) M12 3 −0.008 (±0.058) 37 −0.004 (±0.053)rs111590482 16:4064368 0.125 M06 3 −0.015 (±0.035) 46 −0.006 (±0.039)M12 3 −0.008 (±0.058) 37 −0.002 (±0.047) rs4786454 16:4076136 0.168 M068 −0.020 (±0.046) 59 −0.007 (±0.040) M12 7 −0.049 (±0.122) 50 −0.005(±0.046) rs2283497 16:4066061 0.393 M06 31 −0.005 (±0.053) 88 −0.001(±0.038) M12 27 −0.006 (±0.058) 80   0.005 (±0.049) rs2531967 16:40524860.231 M06 13 −0.007 (±0.024) 68 −0.008 (±0.042) M12 12 −0.031 (±0.086)57 −0.006 (±0.053) rs3730119 16:4057603 0.177 M06 6   0.006 (±0.103) 49−0.002 (±0.050) M12 6 −0.028 (±0.087) 47   0.004 (±0.052) rs1333767516:4077178 0.247 M06 7   0.016 (±0.107) 66   0.002 (±0.044) M12 8 −0.011(±0.115) 62   0.005 (±0.042) dal-PLAQUE-2 Homozygotes for major alleleMean (±STD) P dal-OUTCOMES SNP N mm value³ P value⁴ HR⁴ Origin⁵rs1967309 62   0.006 (±0.047) 0.114 2.41 × 10⁻⁸ 0.651 GWAS 60   0.005(±0.042) (0.560, 0.757) rs2531971 54   0.008 (±0.042) 0.1415 7.74 × 10⁻⁸0.664 Sequenom 52 −0.002 (±0.059) (0.572, 0.771) rs2238448 48   0.011(±0.043) 0.009 8.88 × 10⁻⁸ 0.671 Sequenom 46   0.009 (±0.038) (0.58,0.777) rs11647778 48   0.011 (±0.043) 0.0087 1.72 × 10⁻⁷ 0.678 Sequenom47   0.008 (±0.040) (0.586, 0.784) rs12599911 48   0.011 (±0.044) 0.02051.72 × 10⁻⁷ 0.674 Sequenom 46   0.010 (±0.038) (0.582, 0.782) rs1259585748   0.011 (±0.044) 0.0193 2.02 × 10⁻⁷ 0.677 GWAS 46   0.010 (±0.038)(0.584, 0.784) rs12920508 62   0.006 (±0.047) 0.114 3.18 × 10⁻⁷ 0.669Sequenom 60   0.005 (±0.042) (0.574, 0.781) rs2239310 71   0.004(±0.041) 0.6456 9.58 × 10⁻⁷ 0.674 GWAS 67   0.001 (±0.051) (0.576,0.789) rs11647828 56   0.011 (±0.041) 0.0051 1.32 × 10⁻⁶ 0.696 GWAS 54  0.009 (±0.038) (0.601, 0.806) rs8049452 63 −0.008 (±0.054) 0.0126 1.93× 10⁻⁶ 1.413 GWAS 56 −0.013 (±0.069) (1.225, 1.629) rs12935810 70 −0.006(±0.053) 0.0186 1.03 × 10⁻⁵ 1.377 GWAS 63 −0.007 (±0.069) (1.194, 1.587)rs8061182 67 −0.009 (±0.054) 0.0182 4.72 × 10⁻⁵ 1.343 GWAS 60 −0.014(±0.067) (1.165, 1.547) rs74702385 142   0.002 (±0.048) 0.3881 7.31 ×10⁻⁵ 0.599 GWAS 136 −0.001 (±0.055) (0.465, 0.772) rs17136707 142  0.002 (±0.048) 0.3249 7.40 × 10⁻⁵ 0.594 GWAS 136 −0.001 (±0.054)(0.459, 0.768) rs111590482 142   0.002 (±0.048) 0.3881 1.25 × 10⁻⁴ 0.606GWAS 136 −0.001 (±0.055) (0.469, 0.783) rs4786454 124   0.004 (±0.047)0.0222 1.91 × 10⁻⁴ 0.668 GWAS 119   0.003 (±0.049) (0.540, 0.825)rs2283497 72   0.001 (±0.050) 0.9875 5.23 × 10⁻⁴ 0.766 GWAS 69 −0.007(±0.055) (0.659, 0.891) rs2531967 110   0.005 (±0.048) 0.0184 6.67 ×10⁻⁴ 0.734 GWAS 107   0.004 (±0.048) (0.615, 0.877) rs3730119 136 −0.000(±0.040) 0.8982 9.61 × 10⁻³ 0.763 GWAS 123 −0.002 (±0.052) (0.621,0.936) rs13337675 118 −0.003 (±0.041) 0.1915 4.02 × 10⁻² 0.834 GWAS 106−0.005 (±0.053) (0.702, 0.992) GWAS: genome-wide association study; HR:hazards ratio; MAF: minor allele frequency; OR: odds ratio; SNP: singlenucleotide polymorphism; M06, M12: measures after 6 and 12 months ofdalcetrapib treatment. ¹Position of variants from NCBI Build GRCh37assembly ²Calculated using 386 samples from the dal-Plaque-2 studypopulation ³Calculated using a mixed regression model for measures ofcIMT at 6 and 12 months with adjustment for baseline values ⁴Coxproportional hazards model analyzed in SAS with adjustment for genderand 5 principal components for genetic ancestry and reporting the HR forthe additive genetic model for increasing copies of the minor allele.⁵Results based on genotyped SNPs from the OMNI2.5, and from the Sequenompanel for those that had been imputed. † HR > 1 indicate thathomozygotes for the minor allele are more at risk than homozygotes forthe major allele.at this SNP

Statistical Analyses for Both Examples 1 and 2

Genome-wide association tests were performed using JMP Genomics softwareversion 6.1. significant results were validated in SAS software (v. 9.3)(SAS Institute Inc., Cary, N.C., USA). The 1-degree of freedom additivegenetic test was used where genotypes were coded as 0, 1 or 2, accordingto the count of minor alleles. In the presence of covariates, the Pvalue for the additive genetic test is adjusted for the covariate suchthat

${\log ( \frac{r}{1 - r} )} = {b_{0} + {b_{1}{add}} + {\sum\limits_{j}{b_{j}{cov}_{j}\mspace{14mu} {or}}}}$${{\log ( {{event}\mspace{14mu} {rate}} )} = {b_{0} + {b_{1}{add}} + {\sum\limits_{j}{b_{j}{cov}_{j}}}}};$

where r is the probability of having the event and where the null (H₀)under the additive genetic test is of b₁=0. A Cox proportional hazardsregression model was used to test for gene-by-treatment interactionaccording to: log (event rate) ˜genotype+treatmentarm+genotype*treatment arm+sex+principal components, using bothtreatment and placebo arm samples. The GWAS discovery models includedadjustment for sex and the 5 principal components for genetic ancestry.MAF were calculated using samples from both treatment arms. Rarevariants (MAF<0.05) were analyzed jointly within genes using thesequence kernel association test (SKAT) (Wu M C et al, Am J Hum Genet2011; 89:82-93). including covariates and using a beta-weightingfunction with parameters a₁ set to 1 and a₂ set to 25. Variantspositioned between two genes were analyzed as a distinct set.

For the dal-Plaque-2 population, mixed regression models for repeatedmeasures analysis were tested in SAS software. The dal-Plaque-2 testedendpoint was the mean of IMT measures of common carotid arteries at the6-month and the 12-month visits, using the baseline measure ascovariate. Adjustment of the significance threshold for multiple testingof the 27 SNPs genotyped on the Sequenom panel was not performed, due tothe highly correlated nature of the selected SNPs. As reference, thenumber of independent tests (M_(eff)) was estimated using the method ofGao et al, Genet Epidemiol 2008; 32:361-9. to M_(eff)=8, using thedal-Outcomes population sample.

For the linkage disequilibrium plots (FIGS. 8 and 9), Haploview (version4.2) (Barrett J C et al. Bioinformatics 2005; 21:263-5) was used todisplay linkage disequilibrium r² values in a pair-wise matrix plot witha colour heat plot of D′ values. Blocks of linkage disequilibrium wereconstructed using the confidence interval method set to [0.70, 0.98],upper confidence maximum for strong recombination 0.9 and the fractionof strong LD in informative comparisons ≥0.95.

1. A method for identifying a subject who would benefit fromadministration of a HDL-raising or HDL mimicking agent, the methodcomprising determining a genotype of said subject at one or more ofpolymorphic sites in the subject's ADCY9 gene, wherein at least onepolymorphic site is rs11647778.
 2. The method of claim 1, wherein thegenotype at polymorphic sites selected from: rs1967309, rs12595857,rs2239310, rs11647828, rs8049452, rs12935810, rs74702385, rs17136707,rs8061182, rs111590482, rs4786454, rs2283497, rs2531967, rs3730119,rs13337675, rs12920508, rs12599911, rs2531971 and rs2238448 is alsodetermined.
 3. The method of claim 1, wherein the genotype atpolymorphic sites selected from: rs1967309, rs12595857, rs2239310,rs11647828, rs8049452, rs12935810, rs74702385, rs17136707, rs8061182,rs111590482, rs4786454, rs2283497, rs2531967, rs3730119 and rs13337675is also determined.
 4. The method of claim 1, wherein the genotype atpolymorphic site rs1967309 or rs12595857 is also determined.
 5. Themethod of claim 1, wherein the genotype at rs1967309 is also determined.6. The method of claim 1, wherein the genotype CC at rs11647778 in thesubject's ADCY9 gene is indicative that the subject would benefit fromadministration of an HDL-raising or HDL mimicking agent.
 7. The methodof claim 1, wherein HDL-raising or HDL mimicking agent is niacin,fibrates, glitazone, dalcetrapib, anacetrapib, evacetrapib, DEZ-001,ATH-03, DRL-17822, DLBS-1449, RVX-208, CSL-112, CER-001 orApoA1-Milnano.
 8. The method of claim 1, wherein HDL-raising or HDLmimicking agent is a CETP inhibitor/modulator.
 9. The method of claim 1,wherein HDL-raising or HDL mimicking agent is dalcetrapib, anacetrapib,evacetrapib, DEZ-001, ATH-03, DRL-17822 or DLBS-1449.
 10. The method ofclaim 1, wherein HDL-raising or HDL mimicking agent isS-(2-{[1-(2-ethyl-butyl)-cyclohexanecarbonyl]-amino}-phenyl) ester. 11.The method of claim 1, further comprising administering a HDL-raising orHDL mimicking agent to say subject.
 12. The method of claim 1, whereinthe subject benefiting, have cardiovascular disorder.
 13. A method oftreating cardiovascular disorder in a subject in need thereof, themethod comprising: (a) selecting a subject having an improved responsegenotype at rs11647778 and optionally at one or more of the followingsites: rs1967309, rs12595857, rs2239310, rs11647828, rs8049452,rs12935810, rs74702385, rs17136707, rs8061182, rs111590482, rs4786454,rs2283497, rs2531967, rs3730119, rs2238448, and rs13337675; and (b)administering to said subject a HDL-raising or HDL mimicking agent. 14.The method of claim 1, wherein cardiovascular disorder isatherosclerosis, peripheral vascular disease, dyslipidemia,hyperbetalipoproteinemia, hypoalphalipoproteinemia,hypercholesterolemia, hypertriglyceridemia,familial-hypercholesterolemia, angina, ischemia, cardiac ischemia,stroke, myocardial infarction, reperfusion injury, angioplasticrestenosis, hypertension, and vascular complications of diabetes,obesity or endotoxemia.
 15. The method of claim 1, wherein thecardiovascular disorder is cardiovascular disease, coronary heartdisease, coronary artery disease, hypoalphalipoproteinemia,hyperbetalipoproteinemia, hypercholesterolemia, hyperlipidemia,atherosclerosis, hypertension, hypertriglyceridemia,hyperlipidoproteinemia, peripheral vascular disease, angina, ischemia,or myocardial infarction.
 16. The method of claim 13, wherein anadditional site is rs1967309 or rs12595857.
 17. The method of claim 13,wherein the additional site is rs1967309.
 18. The method of claim 13,wherein a subject having an improved response genotype is CC atrs11647778.
 19. The method of claim 13, wherein a subject having animproved response genotype is CC at rs11647778 and AA at rs1967309. 20.The method of claim 13, wherein the HDL-raising or HDL mimicking agentis a CETP modulator.
 21. The method of claim 13, wherein the HDL-raisingor HDL mimicking agent isS-(2-{[1-(2-ethyl-butyl)-cyclohexanecarbonyl]-amino}-phenyl) ester. 22.The method of claim 13, wherein the improved genotype is CC atrs11647778.
 23. The method of claim 13, wherein the subject has improvedresponse genotype at rs1647778 and rs1967309.
 24. The method of claim13, wherein the improved response genotype is CC at rs11647778 and AA atrs1967309.
 25. The method of claim 13, wherein the cardiovasculardisorder is atherosclerosis, peripheral vascular disease, dyslipidemia,hyperbetalipoproteinemia, hypoalphalipoproteinemia,hypercholesterolemia, hypertriglyceridemia,familial-hypercholesterolemia, angina, ischemia, cardiac ischemia,stroke, myocardial infarction, reperfusion injury, angioplasticrestenosis, hypertension, and vascular complications of diabetes,obesity or endotoxemia.
 26. The method of claim 13, wherein thecardiovascular disorder cardiovascular disease, coronary heart disease,coronary artery disease, hypoalphalipoproteinemia,hyperbetalipoproteinemia, hypercholesterolemia, hyperlipidemia,atherosclerosis, hypertension, hypertriglyceridemia,hyperlipidoproteinemia, peripheral vascular disease, angina, ischemia,or myocardial infarction.
 27. The method of claim 13, wherein theHDL-raising or mimicking agent is a HDL-raising agent, particularly aCETP inhibitor/modulator, more particularly is-(2-{[1-(2-ethyl-butyl)-cyclohexanecarbonyl]-amino}-phenyl) ester.
 28. Amethod of predicting whether a cardiovascular disorder patient has anincreased likelihood of benefiting from treatment with a HDL-raising orHDL mimicking agent, the method comprising screening a sample isolatedfrom said patient for a genetic marker in the Adenylate Cyclase Type 9gene (ADCY9) that is rs11647778/CC and optionally rs12595857/GG,rs1967309/AA, rs111590482/AG, rs111590482/GG, rs11647828/GG,rs12935810/GG, rs17136707/GG, rs2239310/GG, rs2283497/AA, rs2531967/AA,rs3730119/AA, rs4786454/AA, rs74702385/GA, rs74702385/AA, rs8049452/GG,rs2238448/TT or rs8061182/AA, wherein the patient has an increasedlikelihood of benefiting from said treatment.
 29. The method of claim28, wherein said the genetic marker is rs1647778/CC and optionallyrs12595857/GG or rs1967309/AA.
 30. A method of selecting a patient witha cardiovascular disorder as likely to respond to a therapy comprisingHDL-raising or HDL mimicking agent, the method comprising a. detectingan CC genotype at rs11647778 in a sample from the patient, and b.selecting the patient as more likely to respond to a therapy comprisingHDL-raising or HDL mimicking agent when the CC genotype at rs11647778 isdetected in the sample from the patient.
 31. A method of selecting apatient with a cardiovascular disorder as likely to respond to a therapycomprising HDL-raising or HDL mimicking agent, the method comprising a.detecting CC genotype at rs1647778 and AA genotype at rs1967309 in asample from the patient, and b. selecting the patient as more likely torespond to a therapy comprising HDL-raising or HDL mimicking agent whenthe CC genotype at rs11647778 and AA genotype at rs1967309 are detectedin the sample from the patient.
 32. The method of claim 31, wherein thepresence of an CC genotype at rs11647778 in a reference sample indicatesthat the patient is more likely to respond to the therapy with aHDL-raising or HDL mimicking agent.
 33. The method of claim 31, whereinthe presence of CC genotype at rs11647778 and AA genotype at rs1967309in a reference sample indicates that the patient is more likely torespond to the therapy with a HDL-raising or HDL mimicking agent. 34.The method of claim 31 which further comprises c) selecting the therapycomprising a HDL-raising or HDL mimicking agent.
 35. The method of claim31, wherein detecting rs11647778 is done by detecting rs11647778 in asample from the patient, contacting the sample with a reagent (such asprobes or primers) that binds to rs11647778, thereby forming a complexbetween the reagent and rs11647778, detecting the complex formed, andthereby detecting rs11647778.
 36. A method for determining the prognosisof a clinical response in a human patient to a HDL-raising or HDLmimicking agent, comprising determining the presence of at least onepolymorphism in the ADCY9 gene of the patient in which the polymorphismsite is associated with a delayed, partial sub-optimal or lackingclinical response to said HDL-raising or mimicking agent wherein at theleast one polymorphism site is rs11647778.
 37. The method of claim 36,further comprising determining the presence of a second polymorphism inthe ADCY9 gene of the patient in which the polymorphism site isassociated with a delayed, partial sub-optimal or lacking clinicalresponse to said HDL-raising or mimicking agent, wherein the secondpolymorphism site is rs1967309.
 38. The method of claim 36, wherein thepolymorphism is determined by a genotyping analysis.
 39. The method ofclaim 38, wherein the genotyping analysis comprises performingmicroarray analysis or a mass-spectrometric analysis or the use ofpolymorphism-specific primers and/or probes, in particular a primerextension reaction.
 40. The method of claim 36, wherein the HDL-raisingor HDL mimicking agent is a HDL-raising agent.
 41. The method of claim36, wherein the HDL-raising or HDL mimicking agent is a CETP modulator.42. The method of claim 36, wherein the HDL-raising or HDL mimickingagent is dalcetrapib, anacetrapib, evacetrapib, DEZ-001, ATH-03,DRL-17822 or DLBS-1449.
 43. The method of claim 36, wherein theHDL-raising or HDL mimicking agent isS-(2-{[1-(2-ethyl-butyl)-cyclohexanecarbonyl]-amino}-phenyl) ester. 44.The method of claim 1, wherein the HDL-raising or HDL mimicking agent isa compound which increases the HDL level by: CETP modulation, PPARagonism, LXR agonism, HM74 agonism (niacin receptor) thyrotropin hormonereceptor agonism, inhibition of lipases, or HDL catabolism ApoA1inducement.
 45. A method for treating or preventing a cardiovasculardisorder, comprising administering to a subject in need thereof anamount of a HDL-raising or HDL mimicking agent that is effective totreat or prevent the cardiovascular disorder wherein the subject has animproved response genotype at least at rs11647778 and optionally at oneor more of the following sites: rs1967309, rs12595857, rs2239310,rs11647828, rs8049452, rs12935810, rs74702385, rs17136707, rs8061182,rs111590482, rs4786454, rs2283497, rs2531967, rs3730119, rs2238448 andrs13337675.
 46. A method for treating or preventing a cardiovasculardisorder, comprising administering to a subject in need thereof anamount of a HDL-raising or HDL mimicking agent that is effective totreat or prevent the cardiovascular disorder wherein the subject has theCC genotype at rs11647778 and optionally rs12595857/GG, rs1967309/AA,rs111590482/AG, rs111590482/GG, rs11647828/GG, rs12935810/GG,rs7136707/GG, rs2239310/GG, rs2283497/AA, rs2531967/AA, rs3730119/AA,rs4786454/AA, rs74702385/GA, rs74702385/AA, rs8049452/GG and/orrs8061182/AA.
 47. The method of claim 45, wherein the cardiovasculardisorder is atherosclerosis, peripheral vascular disease, dyslipidemia,hyperbetalipoproteinemia, hypoalphalipoproteinemia,hypercholesterolemia, hypertriglyceridemia,familial-hypercholesterolemia, angina, ischemia, cardiac ischemia,stroke, myocardial infarction, reperfusion injury, angioplasticrestenosis, hypertension, and vascular complications of diabetes,obesity or endotoxemia.
 48. The method of claim 45, wherein thecardiovascular disorder is cardiovascular disease, coronary heartdisease, coronary artery disease, hypoalphalipoproteinemia,hyperbetalipoproteinemia, hypercholesterolemia, hyperlipidemia,atherosclerosis, hypertension, hypertriglyceridemia,hyperlipidoproteinemia, peripheral vascular disease, angina, ischemia ormyocardial infarction.
 49. The method of claim 45, wherein the subjecthas an improved response genotype at least at rs11647778 and rs1967309or rs12595857.
 50. The method of claim 45, wherein the subject has animproved response genotype at least at rs11647778 and rs1967309.
 51. Amethod for treating or preventing a cardiovascular disorder, comprisingadministering to a patient having an improved response genotype atrs11647778 and optionally at one or more of the following sites:rs1967309, rs12595857, rs2239310, rs11647828, rs8049452, rs12935810,rs74702385, rs17136707, rs8061182, rs111590482, rs4786454, rs2283497,rs2531967, rs3730119, rs13337675, an amount of a HDL-raising or HDLmimicking agent that is effective to treat or prevent the cardiovasculardisorder.
 52. The method of claim 51, wherein the cardiovasculardisorder is atherosclerosis, peripheral vascular disease, dyslipidemia,hyperbetalipoproteinemia, hypoalphalipoproteinemia,hypercholesterolemia, hypertriglyceridemia,familial-hypercholesterolemia, angina, ischemia, cardiac ischemia,stroke, myocardial infarction, reperfusion injury, angioplasticrestenosis, hypertension, and vascular complications of diabetes,obesity or endotoxemia.
 53. The method of claim 51, wherein thecardiovascular disorder is cardiovascular disease, coronary heartdisease, coronary artery disease, hypoalphalipoproteinemia,hyperbetalipoproteinemia, hypercholesterolemia, hyperlipidemia,atherosclerosis, hypertension, hypertriglyceridemia,hyperlipidoproteinemia, peripheral vascular disease, angina, ischemia ormyocardial infarction.
 54. The method of claim 51, wherein theHDL-raising or HDL mimicking agent is niacin, fibrates, glitazone,dalcetrapib, anacetrapib, evacetrapib, DEZ-001, ATH-03, DRL-17822,DLBS-1449, RVX-208, CSL-112, CER-001 or ApoA1-Milnano.
 55. The method ofclaim 51, wherein the HDL-raising or HDL mimicking agent is a CETPmodulator.
 56. The method of claim 51, wherein the HDL-raising or HDLmimicking agent is dalcetrapib, anacetrapib, evacetrapib, DEZ-001,ATH-03, DRL-17822 or DLBS-1449.
 57. The method of claim 51, wherein theHDL-raising or HDL mimicking agent isS-(2-{[1-(2-ethyl-butyl)-cyclohexanecarbonyl]-amino}-phenyl) ester.